DAZAP1 RNA-Seq in K562

General Information


RBP	DAZAP1
Cell_Line	K562
Method	shRNA
Exp_Name	DAZAP1-BGKLV13-K562
ENCODE_series_ID	ENCSR085PFY
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR907UTB
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	DAZAP1_BGKLV13_37
Rep2	DAZAP1_BGKLV13_38
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	59.7
Rep2_qPCR	61.8
Rep1_WB	80.6
Rep2_WB	82.1
Antibody Cat#	A303-983A
Antibody Lot#	A303-983A
Antibody DCC ID	ENCAB490FGZ
Status	Released
Project	ENCODE3
ID	370

Experiment Information (Status: Released)

	BGKLV13-37	BGKLV13-37	BGKLV13-37	BGKLV13-38	BGKLV13-38	BGKLV13-38
idx	172	172	172	173	173	173
TRCN#_or_BGC#	TRCN0000158588	TRCN0000158588	TRCN0000158588	TRCN0000158588	TRCN0000158588	TRCN0000158588
shRNA_or_gRNA_sequence	CAGGGAATACTTCAAGAAGTT	CAGGGAATACTTCAAGAAGTT	CAGGGAATACTTCAAGAAGTT	CAGGGAATACTTCAAGAAGTT	CAGGGAATACTTCAAGAAGTT	CAGGGAATACTTCAAGAAGTT
PAM
Name	DAZAP1	DAZAP1	DAZAP1	DAZAP1	DAZAP1	DAZAP1
Sample_ID	BGKLV13-37	BGKLV13-37	BGKLV13-37	BGKLV13-38	BGKLV13-38	BGKLV13-38
transduction_Date	6/13/2014	6/13/2014	6/13/2014	6/13/2014	6/13/2014	6/13/2014
days
RBP_name	DAZAP1	DAZAP1	DAZAP1	DAZAP1	DAZAP1	DAZAP1
qPCR_result	59.7	59.7	59.7	61.8	61.8	61.8
Ave_qPCR	60.8	60.8	60.8
RT-qPCR_primer-F	aaggaaggatggcagaaagg	aaggaaggatggcagaaagg	aaggaaggatggcagaaagg
RT-qPCR_primer-R	tccctgagctctgtctcacc	tccctgagctctgtctcacc	tccctgagctctgtctcacc
protein_conc	2149	2149	2149	2196	2196	2196
WB_result	80.6	68.4	80.7	82.1	65.1	76.3
Ave_WB	81.4	66.8	78.5
WB_DONE_date	4/14/2015	6/16/2022	6/28/2022
MW	43kd	43kd	43kd
IP	1			1
antibody_Cat#	A303-983A	A303-984A	A303-985A	A303-983A	lot # 1	lot # 1
Antibody DCC ID	ENCAB490FGZ	ENCAB657IXN	ENCAB554PCA	ENCAB490FGZ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	103.431495	0	0	0	0	0
Rep2_TPM	69.2962584	0	0	0	0	0
Action
Library_start_date	7/27/2014			7/27/2014
repeat_library
Note
ID	187	189	191	188	190	192

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DAZAP1	Product_ID: A303-983A Lot_ID: 1 Source: Bethyl Labs Target Name: DAZAP1-human
DAZAP1	Product_ID: A303-984A Lot_ID: 1 Source: Bethyl Labs Target Name: DAZAP1-human
DAZAP1	Product_ID: A303-985A Lot_ID: 1 Source: Bethyl Labs Target Name: DAZAP1-human

Experiment Status

	BGKLV13-37	BGKLV13-38
Sample_ID	BGKLV13-37	BGKLV13-38
Sample Name	DAZAP1_BGKLV13_37	DAZAP1_BGKLV13_38
Sample Name	DAZAP1_BGKLV13_37	DAZAP1_BGKLV13_38
RBP	DAZAP1	DAZAP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	442	443

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-37	BGKLV13-38
Sample #
Sample Name	DAZAP1-BGKLV13-37	DAZAP1-BGKLV13-38
Sample_Name_Alias	DAZAP1_BGKLV13_37	DAZAP1_BGKLV13_38
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/H3.png	DNA_Library_LV13-14/set1/A4.png
RIN	9.3	9.5
libSample_RNA_Well	RNA_Library_LV12/set1/C12.png	RNA_Library_LV12/set1/D12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-37	BGKLV13-38
RBP	DAZAP1	DAZAP1
Batch_ID	BGKLV13	BGKLV13
WB_result	80.600	82.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2142	2143

Sequencing Information

	BGKLV13-37	BGKLV13-38
Sample_ID	BGKLV13-37	BGKLV13-38
Sample Name	DAZAP1_BGKLV13_37	DAZAP1_BGKLV13_38
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	56,550,000	54,440,000
total_aligned_reads	51,293,494	50,846,702
unique_aligned_reads	47,250,400	46,898,432
percent_uniqueAligned	0.83555	0.86147
correlation_replicates	0.996787	0.996787
spikein_reads	185,266	111,924
percent_spikeins	0.00328	0.00206
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	784	785

Data Submission Information

	BGKLV13-37	BGKLV13-37
ENCODE_alias	brenton-graveley:DAZAP1_BGKLV13	brenton-graveley:DAZAP1-BGKLV13-K562
ENCODE_accession	ENCSR907UTB	ENCSR085PFY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-37	BGKLV13-37
Sample Name	DAZAP1_BGKLV13_37	DAZAP1_BGKLV13_37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2770	6636

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
DAZAP1_BGKLV13_37_ACTGAT_L004_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	784	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13370
DAZAP1_BGKLV13_37_ACTGAT_L004_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	784	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13422
DAZAP1_BGKLV13_37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	784					GRCh38	V40	DAZAP1_BGKLV13_37_ACTGAT_L004_R1_001.fastq.gz,DAZAP1_BGKLV13_37_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	13474
DAZAP1_BGKLV13_37_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	784					GRCh38	V40	DAZAP1_BGKLV13_37/Aligned.sortedByCoord.out.bam		ENCORE2	13526
DAZAP1_BGKLV13_37_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	784					GRCh38	V40	DAZAP1_BGKLV13_37/Aligned.sortedByCoord.out.bam		ENCORE2	13578
DAZAP1_BGKLV13_37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	784					GRCh38	V40	DAZAP1_BGKLV13_37/Aligned.sortedByCoord.out.bam		ENCORE2	13630
DAZAP1_BGKLV13_37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	784					GRCh38	V40	DAZAP1_BGKLV13_37/Aligned.sortedByCoord.out.bam		ENCORE2	13682
DAZAP1_BGKLV13_37_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	784					GRCh38	V40	DAZAP1_BGKLV13_37_ACTGAT_L004_R1_001.fastq.gz,DAZAP1_BGKLV13_37_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	13734
DAZAP1_BGKLV13_38_ATTCCT_L004_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	785	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13371
DAZAP1_BGKLV13_38_ATTCCT_L004_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	785	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13423
DAZAP1_BGKLV13_38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	785					GRCh38	V40	DAZAP1_BGKLV13_38_ATTCCT_L004_R1_001.fastq.gz,DAZAP1_BGKLV13_38_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	13475
DAZAP1_BGKLV13_38_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	785					GRCh38	V40	DAZAP1_BGKLV13_38/Aligned.sortedByCoord.out.bam		ENCORE2	13527
DAZAP1_BGKLV13_38_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	785					GRCh38	V40	DAZAP1_BGKLV13_38/Aligned.sortedByCoord.out.bam		ENCORE2	13579
DAZAP1_BGKLV13_38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	785					GRCh38	V40	DAZAP1_BGKLV13_38/Aligned.sortedByCoord.out.bam		ENCORE2	13631
DAZAP1_BGKLV13_38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	785					GRCh38	V40	DAZAP1_BGKLV13_38/Aligned.sortedByCoord.out.bam		ENCORE2	13683
DAZAP1_BGKLV13_38_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	785					GRCh38	V40	DAZAP1_BGKLV13_38_ATTCCT_L004_R1_001.fastq.gz,DAZAP1_BGKLV13_38_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	13735