DDX19B RNA-Seq in HepG2

General Information


RBP	DDX19B
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX19B-BGHLV31-HepG2
ENCODE_series_ID	ENCSR104QWZ
Batch_ID	BGHLV31
Pool ID	Pool-160229
Local_Set_Name	set31
ENCODE_KD_Exp_ID	ENCSR312SFA
ENCODE_CN_Exp_ID	ENCSR538QOG
Rep1	DDX19B_BGHLV31-25
Rep2	DDX19B_BGHLV31-26
CN1	NT-BGHLV31-1
CN2	NT-BGHLV31-2
Rep1_qPCR	62.4
Rep2_qPCR	65.8
Rep1_WB	83.9
Rep2_WB	85.2
Antibody Cat#	A300-545A
Antibody Lot#	A300-545A
Antibody DCC ID	ENCAB890IXX
Status	Released
Project	ENCODE3
ID	694

Experiment Information (Status: Released)

	BGHLV31-25	BGHLV31-26
idx	773	774
TRCN#_or_BGC#	TRCN0000051129	TRCN0000051129
shRNA_or_gRNA_sequence	CCTGAACTGAAGCTAGCTTAT	CCTGAACTGAAGCTAGCTTAT
PAM
Name	DDX19B	DDX19B
Sample_ID	BGHLV31-25	BGHLV31-26
transduction_Date	9/24/2015	9/24/2015
days
RBP_name	DDX19B	DDX19B
qPCR_result	62.4	65.8
Ave_qPCR	64.1
RT-qPCR_primer-F	ggtaaaacagctgccttcgt
RT-qPCR_primer-R	tttgcccatttgttcaatca
protein_conc	4178	3266
WB_result	83.9	85.2
Ave_WB	84.5
WB_DONE_date	11/20/2015
MW	54kda
IP	1	1
antibody_Cat#	A300-545A	A300-545A
Antibody DCC ID	ENCAB890IXX	ENCAB890IXX
submitted_to_DCC_date	3/8/2016
Rep1_TPM	58.7	0
Rep2_TPM	58.3	0
Action
Library_start_date	2/4/2016	2/4/2016
repeat_library
Note
ID	2866	2867

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX19B	Product_ID: A300-545A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX19B-human

Experiment Status

	BGHLV31-25	BGHLV31-26
Sample_ID	BGHLV31-25	BGHLV31-26
Sample Name	DDX19B_BGHLV31-25	DDX19B_BGHLV31-26
Sample Name	DDX19B_BGHLV31-25	DDX19B_BGHLV31-26
RBP	DDX19B	DDX19B
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-07	2016-03-07
Project	ENCODE3	ENCODE3
Note
ID	1115	1116

Library-Prep
Sequencing

Library-Prep Information

	BGHLV31-25	BGHLV31-26
Sample #
Sample Name	DDX19B-BGHLV31-25	DDX19B-BGHLV31-26
Sample_Name_Alias	DDX19B_BGHLV31-25	DDX19B_BGHLV31-26
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-02-04	2016-02-04
Lib_ID	Lib-160204	Lib-160204
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV31-21B/set1/A6.png	DNA_Library_LV31-21B/set1/B6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/A9.png	RNA_Library_LV29-30-31-32/set1/B9.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV31-25	BGHLV31-26
RBP	DDX19B	DDX19B
Batch_ID	BGHLV31	BGHLV31
WB_result	83.900	85.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2812	2813

Sequencing Information

	BGHLV31-25	BGHLV31-26
Sample_ID	BGHLV31-25	BGHLV31-26
Sample Name	DDX19B_BGHLV31-25	DDX19B_BGHLV31-26
Pool ID	Pool-160229	Pool-160229
LocalServer_folder	set31	set31
total_reads	49,560,120	54,605,004
total_aligned_reads	44,805,618	49,329,270
unique_aligned_reads	42,148,382	46,399,986
percent_uniqueAligned	0.85045	0.84974
correlation_replicates	0.998676	0.998676
spikein_reads	214,562	275,314
percent_spikeins	0.00433	0.00504
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1461	1462

Data Submission Information

	BGHLV31-25	BGHLV31-25
ENCODE_alias	brenton-graveley:DDX19B_BGHLV31	brenton-graveley:DDX19B-BGHLV31-HepG2
ENCODE_accession	ENCSR312SFA	ENCSR104QWZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV31-25	BGHLV31-25
Sample Name	DDX19B_BGHLV31-25	DDX19B_BGHLV31-25
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-07	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3090	6639

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
DDX19B_BGHLV31-25_GTCCGC_L006_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1461	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20976
DDX19B_BGHLV31-25_GTCCGC_L006_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1461	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21002
DDX19B_BGHLV31-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1461					GRCh38	V40	DDX19B_BGHLV31-25_GTCCGC_L006_001.R1.fastq.gz,DDX19B_BGHLV31-25_GTCCGC_L006_001.R2.fastq.gz		ENCORE2	21036
DDX19B_BGHLV31-25_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1461					GRCh38	V40	DDX19B_BGHLV31-25/Aligned.sortedByCoord.out.bam		ENCORE2	21062
DDX19B_BGHLV31-25_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1461					GRCh38	V40	DDX19B_BGHLV31-25/Aligned.sortedByCoord.out.bam		ENCORE2	21088
DDX19B_BGHLV31-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1461					GRCh38	V40	DDX19B_BGHLV31-25/Aligned.sortedByCoord.out.bam		ENCORE2	21114
DDX19B_BGHLV31-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1461					GRCh38	V40	DDX19B_BGHLV31-25/Aligned.sortedByCoord.out.bam		ENCORE2	21140
DDX19B_BGHLV31-25_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1461					GRCh38	V40	DDX19B_BGHLV31-25_GTCCGC_L006_001.R1.fastq.gz,DDX19B_BGHLV31-25_GTCCGC_L006_001.R2.fastq.gz		ENCORE2	21166
DDX19B_BGHLV31-26_GTGAAA_L006_001.R1.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1462	HiSeq2500	100	paired-ended	1				NT-BGHLV31-1_GATCAG_L005_001.R1.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20977
DDX19B_BGHLV31-26_GTGAAA_L006_001.R2.fastq.gz	ENCODE_DATA/set31/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1462	HiSeq2500	100	paired-ended	2				NT-BGHLV31-1_GATCAG_L005_001.R2.fastq.gz,NT-BGHLV31-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	21003
DDX19B_BGHLV31-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1462					GRCh38	V40	DDX19B_BGHLV31-26_GTGAAA_L006_001.R1.fastq.gz,DDX19B_BGHLV31-26_GTGAAA_L006_001.R2.fastq.gz		ENCORE2	21037
DDX19B_BGHLV31-26_Signal.Unique.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1462					GRCh38	V40	DDX19B_BGHLV31-26/Aligned.sortedByCoord.out.bam		ENCORE2	21063
DDX19B_BGHLV31-26_Signal.Unique.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1462					GRCh38	V40	DDX19B_BGHLV31-26/Aligned.sortedByCoord.out.bam		ENCORE2	21089
DDX19B_BGHLV31-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1462					GRCh38	V40	DDX19B_BGHLV31-26/Aligned.sortedByCoord.out.bam		ENCORE2	21115
DDX19B_BGHLV31-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set31/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1462					GRCh38	V40	DDX19B_BGHLV31-26/Aligned.sortedByCoord.out.bam		ENCORE2	21141
DDX19B_BGHLV31-26_quant.sf	ENCODE_DATA/set31/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1462					GRCh38	V40	DDX19B_BGHLV31-26_GTGAAA_L006_001.R1.fastq.gz,DDX19B_BGHLV31-26_GTGAAA_L006_001.R2.fastq.gz		ENCORE2	21167