DAZAP1 RNA-Seq in HepG2

General Information


RBP	DAZAP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	DAZAP1-BGHLV14-HepG2
ENCODE_series_ID	ENCSR946JYH
Batch_ID	BGHLV14
Pool ID	Pool-140901
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR840QFR
ENCODE_CN_Exp_ID	ENCSR003EKR
Rep1	DAZAP1_BGHLV14-7
Rep2	DAZAP1_BGHLV14-8
CN1	NT_BGHLV14-1_1
CN2	NT_BGHLV14-2_1
Rep1_qPCR	30.6
Rep2_qPCR	40.8
Rep1_WB	64.7
Rep2_WB	63.7
Antibody Cat#	A303-983A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB490FGZ
Status	Archived
Project	ENCODE3
ID	386

Experiment Information (Status: Released)

	BGHLV14-7	BGHLV14-8
idx	101	102
TRCN#_or_BGC#	TRCN0000158588	TRCN0000158588
shRNA_or_gRNA_sequence	CAGGGAATACTTCAAGAAGTT	CAGGGAATACTTCAAGAAGTT
PAM
Name	DAZAP1	DAZAP1
Sample_ID	BGHLV14-7	BGHLV14-8
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	DAZAP1	DAZAP1
qPCR_result	30.6	40.8
Ave_qPCR	35.7
RT-qPCR_primer-F	aaggaaggatggcagaaagg
RT-qPCR_primer-R	tccctgagctctgtctcacc
protein_conc	3605	3514
WB_result	64.7	63.7
Ave_WB	64.2
WB_DONE_date	4/14/2015	see BGHLV23
MW
IP	1	1
antibody_Cat#	A303-983A	A303-983A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	57.8	0
Rep2_TPM	49.8	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	2158	2159

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV14-7	BGHLV14-8
Sample_ID	BGHLV14-7	BGHLV14-8
Sample Name	DAZAP1_BGHLV14-7	DAZAP1_BGHLV14-8
Sample Name	DAZAP1_BGHLV14-7	DAZAP1_BGHLV14-8
RBP	DAZAP1	DAZAP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	494	495

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-7	BGHLV14-8
Sample #
Sample Name	DAZAP1-BGHLV14-7	DAZAP1-BGHLV14-8
Sample_Name_Alias	DAZAP1_BGHLV14-7	DAZAP1_BGHLV14-8
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/D8.png	DNA_Library_LV13-14/set1/E8.png
RIN	9.7	9.4
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/G4.png	RNA_Library_LV13-14-16/set1/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-7	BGHLV14-8
RBP	DAZAP1	DAZAP1
Batch_ID	BGHLV14	BGHLV14
WB_result	64.700	63.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2178	2179

Sequencing Information

	BGHLV14-7	BGHLV14-8
Sample_ID	BGHLV14-7	BGHLV14-8
Sample Name	DAZAP1_BGHLV14-7	DAZAP1_BGHLV14-8
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set14	set14
total_reads	43,820,000	43,180,000
total_aligned_reads	40,634,360	40,239,994
unique_aligned_reads	38,564,668	38,174,502
percent_uniqueAligned	0.88007	0.88408
correlation_replicates	0.999343	0.999343
spikein_reads	156,184	119,934
percent_spikeins	0.00356	0.00278
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	820	821

Data Submission Information

	BGHLV14-7	BGHLV14-7
ENCODE_alias	brenton-graveley:DAZAP1_BGHLV14	brenton-graveley:DAZAP1-BGHLV14-HepG2
ENCODE_accession	ENCSR840QFR	ENCSR946JYH
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-7	BGHLV14-7
Sample Name	DAZAP1_BGHLV14-7	DAZAP1_BGHLV14-7
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2796	6634

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_BGHLV14-7_GGCTAC_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	820	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13786
DAZAP1_BGHLV14-7_GGCTAC_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	820	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13848
DAZAP1_BGHLV14-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	820					GRCh38	V40	DAZAP1_BGHLV14-7_GGCTAC_L008_R1_001.fastq.gz,DAZAP1_BGHLV14-7_GGCTAC_L008_R2_001.fastq.gz		ENCORE2	13910
DAZAP1_BGHLV14-7_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	820					GRCh38	V40	DAZAP1_BGHLV14-7/Aligned.sortedByCoord.out.bam		ENCORE2	13972
DAZAP1_BGHLV14-7_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	820					GRCh38	V40	DAZAP1_BGHLV14-7/Aligned.sortedByCoord.out.bam		ENCORE2	14034
DAZAP1_BGHLV14-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	820					GRCh38	V40	DAZAP1_BGHLV14-7/Aligned.sortedByCoord.out.bam		ENCORE2	14096
DAZAP1_BGHLV14-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	820					GRCh38	V40	DAZAP1_BGHLV14-7/Aligned.sortedByCoord.out.bam		ENCORE2	14158
DAZAP1_BGHLV14-7_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	820					GRCh38	V40	DAZAP1_BGHLV14-7_GGCTAC_L008_R1_001.fastq.gz,DAZAP1_BGHLV14-7_GGCTAC_L008_R2_001.fastq.gz		ENCORE2	14220
DAZAP1_BGHLV14-8_CTTGTA_L008_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	821	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13787
DAZAP1_BGHLV14-8_CTTGTA_L008_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	821	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13849
DAZAP1_BGHLV14-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	821					GRCh38	V40	DAZAP1_BGHLV14-8_CTTGTA_L008_R1_001.fastq.gz,DAZAP1_BGHLV14-8_CTTGTA_L008_R2_001.fastq.gz		ENCORE2	13911
DAZAP1_BGHLV14-8_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	821					GRCh38	V40	DAZAP1_BGHLV14-8/Aligned.sortedByCoord.out.bam		ENCORE2	13973
DAZAP1_BGHLV14-8_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	821					GRCh38	V40	DAZAP1_BGHLV14-8/Aligned.sortedByCoord.out.bam		ENCORE2	14035
DAZAP1_BGHLV14-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	821					GRCh38	V40	DAZAP1_BGHLV14-8/Aligned.sortedByCoord.out.bam		ENCORE2	14097
DAZAP1_BGHLV14-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	821					GRCh38	V40	DAZAP1_BGHLV14-8/Aligned.sortedByCoord.out.bam		ENCORE2	14159
DAZAP1_BGHLV14-8_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	821					GRCh38	V40	DAZAP1_BGHLV14-8_CTTGTA_L008_R1_001.fastq.gz,DAZAP1_BGHLV14-8_CTTGTA_L008_R2_001.fastq.gz		ENCORE2	14221