ZNF335 RNA-Seq in K562

General Information


RBP	ZNF335
Cell_Line	K562
Method	CRISPR
Exp_Name	ZNF335-BGKcLV17-K562
ENCODE_series_ID	ENCSR309BZR
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR650GNB
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	ZNF335-BGKcLV17-57
Rep2	ZNF335-BGKcLV17-58
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	30.1
Rep2_qPCR	33.5
Rep1_WB	51.2
Rep2_WB	59.6
Antibody Cat#	PA5-67158
Antibody Lot#	lot# UC2731469A
Antibody DCC ID	ENCAB644YFO
Status	Released
Project	ENCODE4
ID	96

Experiment Information (Status: Released)

	BGKcLV17-57	BGKcLV17-58
idx	666	667
TRCN#_or_BGC#	BGC#0000447	BGC#0000447
shRNA_or_gRNA_sequence	CTGGTAAAAAAGGACGTCTA	CTGGTAAAAAAGGACGTCTA
PAM	CGG	CGG
Name	ZNF335_89	ZNF335_89
Sample_ID	BGKcLV17-57	BGKcLV17-58
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	ZNF335	ZNF335
qPCR_result	30.1	33.5
Ave_qPCR	31.8
RT-qPCR_primer-F	AGAGCCAAGAGGAAGAGGGA
RT-qPCR_primer-R	GGCTCATCCTCAGCTGGATT
protein_conc	4743	5038
WB_result	51.2	59.6
Ave_WB	55.4
WB_DONE_date	9/6/19	WES
MW	145KD
IP	Rabbit / I	Polyclonal
antibody_Cat#	PA5-67158	lot# UC2731469A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	10	0
Rep2_TPM	6.7	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4786	4787

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ZNF335	Product_ID: PA5-67158 Lot_ID: UC2731469A Source: Thermo Fisher Target Name: ZNF335-human

Experiment Status

	BGKcLV17-57	BGKcLV17-58
Sample_ID	BGKcLV17-57	BGKcLV17-58
Sample Name
Sample Name	ZNF335-BGKcLV17-57	ZNF335-BGKcLV17-58
RBP	ZNF335	ZNF335
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5525	5526

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-57	BGKcLV17-58
Sample #	115	116
Sample Name	ZNF335-BGKcLV17-57	ZNF335-BGKcLV17-58
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	2-G2	2-H2
Tecan	23.83	28.28
Tecan_date	2019-12-16	2019-12-16
Size_bp	276	273
Peak_Molarity	17.50	22.00
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/G10.png	DNA_Library_set43-44/set1/H10.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set43-44/set4/G5.png	RNA_Library_set43-44/set4/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-57	BGKcLV17-58
RBP	ZNF335	ZNF335
Batch_ID	BGKcLV17	BGKcLV17
WB_result	51.200	59.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	691	692

Sequencing Information

	BGKcLV17-57	BGKcLV17-58
Sample_ID	BGKcLV17-57	BGKcLV17-58
Sample Name	ZNF335-BGKcLV17-57	ZNF335-BGKcLV17-58
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	265,455,298	124,870,786
total_aligned_reads	260,870,574	118,838,706
unique_aligned_reads	236,605,062	108,271,304
percent_uniqueAligned	0.89132	0.86707
correlation_replicates	0.997492	0.997492
spikein_reads	40,488	33,218
percent_spikeins	0.00015	0.00027
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	197	198

Data Submission Information

	BGKcLV17-57	BGKcLV17-57	BGKcLV17-57	BGKcLV17-57	BGKcLV17-57	BGKcLV17-57	BGKcLV17-58	BGKcLV17-58	BGKcLV17-58	BGKcLV17-58
ENCODE_alias	brenton-graveley:ZNF335-BGKcLV17	brenton-graveley:ZNF335-BGKcLV17-57	brenton-graveley:L-ZNF335-BGKcLV17-57	brenton-graveley:ZNF335-BGKcLV17-57_S25_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZNF335-BGKcLV17-57_S25_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZNF335-BGKcLV17-K562	brenton-graveley:ZNF335-BGKcLV17-58	brenton-graveley:L-ZNF335-BGKcLV17-58	brenton-graveley:ZNF335-BGKcLV17-58_S26_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ZNF335-BGKcLV17-58_S26_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR650GNB	ENCBS464XQN	ENCLB999GRF	ENCFF534NIK	ENCFF117LQQ	ENCSR309BZR	ENCBS362YBE	ENCLB735IRF	ENCFF594BJR	ENCFF232APF
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	BGKcLV17-57	BGKcLV17-57	BGKcLV17-57	BGKcLV17-57	BGKcLV17-57	BGKcLV17-57	BGKcLV17-58	BGKcLV17-58	BGKcLV17-58	BGKcLV17-58
Sample Name	ZNF335-BGKcLV17-57	ZNF335-BGKcLV17-57	ZNF335-BGKcLV17-57	ZNF335-BGKcLV17-57	ZNF335-BGKcLV17-57	ZNF335-BGKcLV17-57	ZNF335-BGKcLV17-58	ZNF335-BGKcLV17-58	ZNF335-BGKcLV17-58	ZNF335-BGKcLV17-58
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		ZNF335-BGKcLV17-57.pdf	L-ZNF335-BGKcLV17-57.pdf				ZNF335-BGKcLV17-58.pdf	L-ZNF335-BGKcLV17-58.pdf
ID	82	244	410	712	742	7370	245	411	713	743

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
ZNF335-BGKcLV17-57_S25_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	197	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	299
ZNF335-BGKcLV17-57_S25_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	197	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	329
ZNF335-BGKcLV17-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	197					GRCh38	V40	ZNF335-BGKcLV17-57_S25_R1_001.filtered.trimmed.paired.fastq.gz,ZNF335-BGKcLV17-57_S25_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24695
ZNF335-BGKcLV17-57_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	197					GRCh38	V40	ZNF335-BGKcLV17-57/Aligned.sortedByCoord.out.bam		ENCORE2	24725
ZNF335-BGKcLV17-57_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	197					GRCh38	V40	ZNF335-BGKcLV17-57/Aligned.sortedByCoord.out.bam		ENCORE2	24755
ZNF335-BGKcLV17-57_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	197					GRCh38	V40	ZNF335-BGKcLV17-57/Aligned.sortedByCoord.out.bam		ENCORE2	24785
ZNF335-BGKcLV17-57_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	197					GRCh38	V40	ZNF335-BGKcLV17-57/Aligned.sortedByCoord.out.bam		ENCORE2	24815
ZNF335-BGKcLV17-57_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	197					GRCh38	V40	ZNF335-BGKcLV17-57_S25_R1_001.filtered.trimmed.paired.fastq.gz,ZNF335-BGKcLV17-57_S25_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24845
ZNF335-BGKcLV17-58_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	198	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	300
ZNF335-BGKcLV17-58_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	198	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	330
ZNF335-BGKcLV17-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	198					GRCh38	V40	ZNF335-BGKcLV17-58_S26_R1_001.filtered.trimmed.paired.fastq.gz,ZNF335-BGKcLV17-58_S26_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24696
ZNF335-BGKcLV17-58_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	198					GRCh38	V40	ZNF335-BGKcLV17-58/Aligned.sortedByCoord.out.bam		ENCORE2	24726
ZNF335-BGKcLV17-58_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	198					GRCh38	V40	ZNF335-BGKcLV17-58/Aligned.sortedByCoord.out.bam		ENCORE2	24756
ZNF335-BGKcLV17-58_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	198					GRCh38	V40	ZNF335-BGKcLV17-58/Aligned.sortedByCoord.out.bam		ENCORE2	24786
ZNF335-BGKcLV17-58_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	198					GRCh38	V40	ZNF335-BGKcLV17-58/Aligned.sortedByCoord.out.bam		ENCORE2	24816
ZNF335-BGKcLV17-58_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	198					GRCh38	V40	ZNF335-BGKcLV17-58_S26_R1_001.filtered.trimmed.paired.fastq.gz,ZNF335-BGKcLV17-58_S26_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24846