ZNF800 RNA-Seq in K562

General Information


RBP	ZNF800
Cell_Line	K562
Method	CRISPR
Exp_Name	ZNF800-BGKcLV06-K562
ENCODE_series_ID	ENCSR611ZYN
Batch_ID	BGKcLV06
Pool ID	Pool-170911
Local_Set_Name	set39_K
ENCODE_KD_Exp_ID	ENCSR974RYS
ENCODE_CN_Exp_ID	ENCSR341TTW
Rep1	ZNF800-BGKcLV06-47
Rep2	ZNF800-BGKcLV06-48
CN1	NT-BGKcLV06-1
CN2	NT-BGKcLV06-2
Rep1_qPCR	96.1
Rep2_qPCR	97.6
Rep1_WB	84.0
Rep2_WB	70.4
Antibody Cat#	A303-283A
Antibody Lot#
Antibody DCC ID	ENCAB214KLU
Status	Released
Project	ENCODE3
ID	781

Experiment Information (Status: Released)

	BGKcLV06-47	BGKcLV06-48
idx	223	224
TRCN#_or_BGC#	BGC#0000070	BGC#0000070
shRNA_or_gRNA_sequence	GTTCACAGCATCCGTGATGA	GTTCACAGCATCCGTGATGA
PAM
Name	ZNF800_81	ZNF800_81
Sample_ID	BGKcLV06-47	BGKcLV06-48
transduction_Date	6/9/17	6/9/17
days	Day 6	Day 6
RBP_name	ZNF800	ZNF800
qPCR_result	96.1	97.6
Ave_qPCR	96.9
RT-qPCR_primer-F	gactgaccaccatcatcacg
RT-qPCR_primer-R	ggttgctgtaacaaaggagga
protein_conc	2935	2637
WB_result	84.0	70.4
Ave_WB	77.2
WB_DONE_date	7/20/17
MW	75KDa
IP
antibody_Cat#	A303-283A
Antibody DCC ID	ENCAB214KLU	ENCAB214KLU
submitted_to_DCC_date	9/29/17
Rep1_TPM	21.2	0
Rep2_TPM	31.8	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	4321	4322

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ZNF800	Product_ID: A303-283A Lot_ID: 1 Source: Bethyl Labs Target Name: ZNF800-human

Experiment Status

	BGKcLV06-47	BGKcLV06-48
Sample_ID	BGKcLV06-47	BGKcLV06-48
Sample Name	ZNF800-BGKcLV06-47	ZNF800-BGKcLV06-48
Sample Name	ZNF800-BGKcLV06-47	ZNF800-BGKcLV06-48
RBP	ZNF800	ZNF800
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1379	1380

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV06-47	BGKcLV06-48
Sample #
Sample Name	ZNF800-BGKcLV06-47	ZNF800-BGKcLV06-48
Sample_Name_Alias	ZNF800-BGKcLV06-47	ZNF800-BGKcLV06-48
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/E3.png	DNA_Library_set39/set2/F3.png
RIN	8.6	10.0
libSample_RNA_Well	RNA_Library_set39/set3/H2.png	RNA_Library_set39/set1/F3.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV06-47	BGKcLV06-48
RBP	ZNF800	ZNF800
Batch_ID	BGKcLV06	BGKcLV06
WB_result	84.000	70.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3074	3075

Sequencing Information

	BGKcLV06-47	BGKcLV06-48
Sample_ID	BGKcLV06-47	BGKcLV06-48
Sample Name	ZNF800-BGKcLV06-47	ZNF800-BGKcLV06-48
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_K	set39_K
total_reads	78,482,920	46,516,548
total_aligned_reads	69,995,296	41,412,772
unique_aligned_reads	63,210,010	37,730,878
percent_uniqueAligned	0.80540	0.81113
correlation_replicates	0.998393	0.998393
spikein_reads	29,146	17,806
percent_spikeins	0.00037	0.00038
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1725	1726

Data Submission Information

	BGKcLV06-47	BGKcLV06-47
ENCODE_alias	brenton-graveley:ZNF800-BGKcLV06	brenton-graveley:ZNF800-BGKcLV06-K562
ENCODE_accession	ENCSR974RYS	ENCSR611ZYN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV06-47	BGKcLV06-47
Sample Name	ZNF800-BGKcLV06-47	ZNF800-BGKcLV06-47
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3229	7055

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
ZNF800-BGKcLV06-47_ACAGTG_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1725	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22496
ZNF800-BGKcLV06-47_ACAGTG_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1725	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22532
ZNF800-BGKcLV06-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1725					GRCh38	V40	ZNF800-BGKcLV06-47_ACAGTG_ACBE67ANXX_L007_001.R1.fastq.gz,ZNF800-BGKcLV06-47_ACAGTG_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22568
ZNF800-BGKcLV06-47_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1725					GRCh38	V40	ZNF800-BGKcLV06-47/Aligned.sortedByCoord.out.bam		ENCORE2	22604
ZNF800-BGKcLV06-47_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1725					GRCh38	V40	ZNF800-BGKcLV06-47/Aligned.sortedByCoord.out.bam		ENCORE2	22640
ZNF800-BGKcLV06-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1725					GRCh38	V40	ZNF800-BGKcLV06-47/Aligned.sortedByCoord.out.bam		ENCORE2	22676
ZNF800-BGKcLV06-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1725					GRCh38	V40	ZNF800-BGKcLV06-47/Aligned.sortedByCoord.out.bam		ENCORE2	22712
ZNF800-BGKcLV06-47_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1725					GRCh38	V40	ZNF800-BGKcLV06-47_ACAGTG_ACBE67ANXX_L007_001.R1.fastq.gz,ZNF800-BGKcLV06-47_ACAGTG_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22748
ZNF800-BGKcLV06-48_GCCAAT_ACBE67ANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1726	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22497
ZNF800-BGKcLV06-48_GCCAAT_ACBE67ANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1726	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22533
ZNF800-BGKcLV06-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1726					GRCh38	V40	ZNF800-BGKcLV06-48_GCCAAT_ACBE67ANXX_L007_001.R1.fastq.gz,ZNF800-BGKcLV06-48_GCCAAT_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22569
ZNF800-BGKcLV06-48_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1726					GRCh38	V40	ZNF800-BGKcLV06-48/Aligned.sortedByCoord.out.bam		ENCORE2	22605
ZNF800-BGKcLV06-48_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1726					GRCh38	V40	ZNF800-BGKcLV06-48/Aligned.sortedByCoord.out.bam		ENCORE2	22641
ZNF800-BGKcLV06-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1726					GRCh38	V40	ZNF800-BGKcLV06-48/Aligned.sortedByCoord.out.bam		ENCORE2	22677
ZNF800-BGKcLV06-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1726					GRCh38	V40	ZNF800-BGKcLV06-48/Aligned.sortedByCoord.out.bam		ENCORE2	22713
ZNF800-BGKcLV06-48_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1726					GRCh38	V40	ZNF800-BGKcLV06-48_GCCAAT_ACBE67ANXX_L007_001.R1.fastq.gz,ZNF800-BGKcLV06-48_GCCAAT_ACBE67ANXX_L007_001.R2.fastq.gz		ENCORE2	22749