DAZAP1 RNA-Seq in HepG2

General Information


RBP	DAZAP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	DAZAP1-BGHLV23-HepG2
ENCODE_series_ID	ENCSR736EJC
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR220TBR
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	DAZAP1-BGHLV23-11
Rep2	DAZAP1-BGHLV23-12
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	76.4
Rep2_qPCR	75.9
Rep1_WB	80.0
Rep2_WB	80.6
Antibody Cat#	A303-983A
Antibody Lot#	A303-983A
Antibody DCC ID	ENCAB490FGZ
Status	Released
Project	ENCODE3
ID	540

Experiment Information (Status: Released)

	BGHLV23-11	BGHLV23-12
idx	503	504
TRCN#_or_BGC#	TRCN0000164245	TRCN0000164245
shRNA_or_gRNA_sequence	CCCAGGAGCGATAACAGTAAA	CCCAGGAGCGATAACAGTAAA
PAM
Name	DAZAP1_45	DAZAP1_45
Sample_ID	BGHLV23-11	BGHLV23-12
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	DAZAP1	DAZAP1
qPCR_result	76.4	75.9
Ave_qPCR	76.2
RT-qPCR_primer-F	aaggaaggatggcagaaagg
RT-qPCR_primer-R	tccctgagctctgtctcacc
protein_conc	5515	6409
WB_result	80.0	80.6
Ave_WB	80.3
WB_DONE_date	4/14/2015
MW
IP	1	1
antibody_Cat#	A303-983A	A303-983A
Antibody DCC ID	ENCAB490FGZ	ENCAB490FGZ
submitted_to_DCC_date	5/4/2015
Rep1_TPM	57.8	0
Rep2_TPM	49.8	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2578	2579

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

Experiment Status

	BGHLV23-11	BGHLV23-12
Sample_ID	BGHLV23-11	BGHLV23-12
Sample Name	DAZAP1-BGHLV23-11	DAZAP1-BGHLV23-12
Sample Name	DAZAP1-BGHLV23-11	DAZAP1-BGHLV23-12
RBP	DAZAP1	DAZAP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	816	817

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-11	BGHLV23-12
Sample #
Sample Name	DAZAP1-BGHLV23-11	DAZAP1-BGHLV23-12
Sample_Name_Alias	DAZAP1-BGHLV23-11	DAZAP1-BGHLV23-12
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/G11.png	DNA_Library_LV20-22-23/set1/H11.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_LV19-21-24/set2/C5.png	RNA_Library_LV19-21-24/set2/D5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-11	BGHLV23-12
RBP	DAZAP1	DAZAP1
Batch_ID	BGHLV23	BGHLV23
WB_result	80.000	80.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2504	2505

Sequencing Information

	BGHLV23-11	BGHLV23-12
Sample_ID	BGHLV23-11	BGHLV23-12
Sample Name	DAZAP1-BGHLV23-11	DAZAP1-BGHLV23-12
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	56,940,000	66,800,000
total_aligned_reads	51,651,704	60,613,296
unique_aligned_reads	48,830,510	57,285,570
percent_uniqueAligned	0.85758	0.85757
correlation_replicates	0.999430	0.999430
spikein_reads	333,624	396,220
percent_spikeins	0.00586	0.00593
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1126	1127

Data Submission Information

	BGHLV23-11	BGHLV23-11
ENCODE_alias	brenton-graveley:DAZAP1-BGHLV23	brenton-graveley:DAZAP1-BGHLV23-HepG2
ENCODE_accession	ENCSR220TBR	ENCSR736EJC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-11	BGHLV23-11
Sample Name	DAZAP1-BGHLV23-11	DAZAP1-BGHLV23-11
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2940	6635

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-BGHLV23-11_ACTGAT_L004_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1126	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16654
DAZAP1-BGHLV23-11_ACTGAT_L004_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1126	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16692
DAZAP1-BGHLV23-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1126					GRCh38	V40	DAZAP1-BGHLV23-11_ACTGAT_L004_R1_001.fastq.gz,DAZAP1-BGHLV23-11_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	16730
DAZAP1-BGHLV23-11_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1126					GRCh38	V40	DAZAP1-BGHLV23-11/Aligned.sortedByCoord.out.bam		ENCORE2	16768
DAZAP1-BGHLV23-11_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1126					GRCh38	V40	DAZAP1-BGHLV23-11/Aligned.sortedByCoord.out.bam		ENCORE2	16806
DAZAP1-BGHLV23-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1126					GRCh38	V40	DAZAP1-BGHLV23-11/Aligned.sortedByCoord.out.bam		ENCORE2	16844
DAZAP1-BGHLV23-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1126					GRCh38	V40	DAZAP1-BGHLV23-11/Aligned.sortedByCoord.out.bam		ENCORE2	16882
DAZAP1-BGHLV23-11_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1126					GRCh38	V40	DAZAP1-BGHLV23-11_ACTGAT_L004_R1_001.fastq.gz,DAZAP1-BGHLV23-11_ACTGAT_L004_R2_001.fastq.gz		ENCORE2	16920
DAZAP1-BGHLV23-12_ATTCCT_L004_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1127	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16655
DAZAP1-BGHLV23-12_ATTCCT_L004_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1127	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16693
DAZAP1-BGHLV23-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1127					GRCh38	V40	DAZAP1-BGHLV23-12_ATTCCT_L004_R1_001.fastq.gz,DAZAP1-BGHLV23-12_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	16731
DAZAP1-BGHLV23-12_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1127					GRCh38	V40	DAZAP1-BGHLV23-12/Aligned.sortedByCoord.out.bam		ENCORE2	16769
DAZAP1-BGHLV23-12_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1127					GRCh38	V40	DAZAP1-BGHLV23-12/Aligned.sortedByCoord.out.bam		ENCORE2	16807
DAZAP1-BGHLV23-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1127					GRCh38	V40	DAZAP1-BGHLV23-12/Aligned.sortedByCoord.out.bam		ENCORE2	16845
DAZAP1-BGHLV23-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1127					GRCh38	V40	DAZAP1-BGHLV23-12/Aligned.sortedByCoord.out.bam		ENCORE2	16883
DAZAP1-BGHLV23-12_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1127					GRCh38	V40	DAZAP1-BGHLV23-12_ATTCCT_L004_R1_001.fastq.gz,DAZAP1-BGHLV23-12_ATTCCT_L004_R2_001.fastq.gz		ENCORE2	16921