DDX47 RNA-Seq in HepG2

General Information


RBP	DDX47
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX47-BGHLV22-HepG2
ENCODE_series_ID	ENCSR891MRP
Batch_ID	BGHLV22
Pool ID	Pool-160425
Local_Set_Name	set22
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID	ENCSR968BBQ
Rep1	DDX47_BGHLV22-9B
Rep2	DDX47_BGHLV22-10B
CN1	NT_BGHLV22-1B
CN2	NT_BGHLV22-2B
Rep1_qPCR	48.1
Rep2_qPCR	44.6
Rep1_WB	80.0
Rep2_WB	88.6
Antibody Cat#	GTX120497
Antibody Lot#	GTX120497
Antibody DCC ID	ENCAB996IKB
Status	Released
Project	ENCODE3
ID	599

Experiment Information (Status: Released)

	BGHLV22-9	BGHLV22-9	BGHLV22-10	BGHLV22-10
idx	437	437	438	438
TRCN#_or_BGC#	TRCN0000005618	TRCN0000005618	TRCN0000005618	TRCN0000005618
shRNA_or_gRNA_sequence	CGAGTTCTGCTGTTCTGTAAA	CGAGTTCTGCTGTTCTGTAAA	CGAGTTCTGCTGTTCTGTAAA	CGAGTTCTGCTGTTCTGTAAA
PAM
Name	DDX47	DDX47	DDX47	DDX47
Sample_ID	BGHLV22-9	BGHLV22-9	BGHLV22-10	BGHLV22-10
transduction_Date	10/16/2014	10/16/2014	10/16/2014	10/16/2014
days
RBP_name	DDX47	DDX47	DDX47	DDX47
qPCR_result	48.1	48.1	44.6	44.6
Ave_qPCR	46.3	46.3
RT-qPCR_primer-F	ACAGAACGCGTCGCTGAAG	ACAGAACGCGTCGCTGAAG
RT-qPCR_primer-R	TATCTCCAGCATCCTCTCGC	TATCTCCAGCATCCTCTCGC
protein_conc	6511	6511	7158	7158
WB_result	80.0	82.4	88.6	87.8
Ave_WB	84.3	85.1
WB_DONE_date	10/20/2015	7/9/19
MW	51kDa	51kDa
IP	1	1	1
antibody_Cat#	GTX120497	A302-976A	GTX120497	lot#1
Antibody DCC ID	ENCAB996IKB		ENCAB996IKB
submitted_to_DCC_date	3/8/2016
Rep1_TPM	5.9	0	0	0
Rep2_TPM	5.6	0	0	0
Action
Library_start_date	3/10/2016		3/10/2016
repeat_library
Note
ID	2504	2506	2505	2507

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX47	Product_ID: GTX120497 Lot_ID: 40387 Source: GeneTex Target Name: DDX47-human
DDX47	Product_ID: A302-976A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX47-human

Experiment Status

	BGHLV22-9	BGHLV22-10
Sample_ID	BGHLV22-9	BGHLV22-10
Sample Name	DDX47_BGHLV22-10B	DDX47_BGHLV22-9B
Sample Name	DDX47_BGHLV22-10B	DDX47_BGHLV22-9B
RBP	DDX47	DDX47
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1207	1208

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-9	BGHLV22-10
Sample #
Sample Name	DDX47-BGHLV22-9B	DDX47-BGHLV22-10B
Sample_Name_Alias	DDX47_BGHLV22-9B	DDX47_BGHLV22-10B
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-10	2016-03-10
Lib_ID	Lib-160310	Lib-160310
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set2/E2.png	DNA_Library_LV33-34-25B-32/set2/F2.png
RIN	9.7	9.5
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/A1.png	RNA_Library_LV22-23-25/set1/B1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-9	BGHLV22-10
RBP	DDX47	DDX47
Batch_ID	BGHLV22	BGHLV22
WB_result	80.000	88.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2885	2884

Sequencing Information

	BGHLV22-9	BGHLV22-10
Sample_ID	BGHLV22-9	BGHLV22-10
Sample Name	DDX47_BGHLV22-9B	DDX47_BGHLV22-10B
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set22	set22
total_reads	82,330,312	88,436,568
total_aligned_reads	64,209,650	70,434,810
unique_aligned_reads	60,282,258	66,025,514
percent_uniqueAligned	0.73220	0.74659
correlation_replicates	0.998611	0.998611
spikein_reads	174,542	190,802
percent_spikeins	0.00212	0.00216
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1534	1533

Data Submission Information

	BGHLV22-9	BGHLV22-9
ENCODE_alias	brenton-graveley:DDX47_BGHLV22	brenton-graveley:DDX47-BGHLV22-HepG2
ENCODE_accession	ENCSR388CNS	ENCSR891MRP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-9	BGHLV22-9
Sample Name	DDX47_BGHLV22-10B	DDX47_BGHLV22-9B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3143	6653

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
DDX47_BGHLV22-9B_ATCACG_L005_001.R1.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1534	HiSeq2000	100	paired-ended	1				NT_BGHLV22-1B_ACTGAT_L005_001.R1.fastq.gz,NT_BGHLV22-2B_ATTCCT_L005_001.R1.fastq.gz	ENCODE3	16277
DDX47_BGHLV22-9B_ATCACG_L005_001.R2.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1534	HiSeq2000	100	paired-ended	2				NT_BGHLV22-1B_ACTGAT_L005_001.R2.fastq.gz,NT_BGHLV22-2B_ATTCCT_L005_001.R2.fastq.gz	ENCODE3	16317
DDX47_BGHLV22-9B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1534					GRCh38	V40	DDX47_BGHLV22-9B_ATCACG_L005_001.R1.fastq.gz,DDX47_BGHLV22-9B_ATCACG_L005_001.R2.fastq.gz		ENCORE2	16415
DDX47_BGHLV22-9B_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1534					GRCh38	V40	DDX47_BGHLV22-9B/Aligned.sortedByCoord.out.bam		ENCORE2	16455
DDX47_BGHLV22-9B_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1534					GRCh38	V40	DDX47_BGHLV22-9B/Aligned.sortedByCoord.out.bam		ENCORE2	16495
DDX47_BGHLV22-9B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1534					GRCh38	V40	DDX47_BGHLV22-9B/Aligned.sortedByCoord.out.bam		ENCORE2	16535
DDX47_BGHLV22-9B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1534					GRCh38	V40	DDX47_BGHLV22-9B/Aligned.sortedByCoord.out.bam		ENCORE2	16575
DDX47_BGHLV22-9B_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1534					GRCh38	V40	DDX47_BGHLV22-9B_ATCACG_L005_001.R1.fastq.gz,DDX47_BGHLV22-9B_ATCACG_L005_001.R2.fastq.gz		ENCORE2	16615
DDX47_BGHLV22-10B_CGATGT_L005_001.R1.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1533	HiSeq2000	100	paired-ended	1				NT_BGHLV22-1B_ACTGAT_L005_001.R1.fastq.gz,NT_BGHLV22-2B_ATTCCT_L005_001.R1.fastq.gz	ENCODE3	16276
DDX47_BGHLV22-10B_CGATGT_L005_001.R2.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1533	HiSeq2000	100	paired-ended	2				NT_BGHLV22-1B_ACTGAT_L005_001.R2.fastq.gz,NT_BGHLV22-2B_ATTCCT_L005_001.R2.fastq.gz	ENCODE3	16316
DDX47_BGHLV22-10B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1533					GRCh38	V40	DDX47_BGHLV22-10B_CGATGT_L005_001.R1.fastq.gz,DDX47_BGHLV22-10B_CGATGT_L005_001.R2.fastq.gz		ENCORE2	16414
DDX47_BGHLV22-10B_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1533					GRCh38	V40	DDX47_BGHLV22-10B/Aligned.sortedByCoord.out.bam		ENCORE2	16454
DDX47_BGHLV22-10B_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1533					GRCh38	V40	DDX47_BGHLV22-10B/Aligned.sortedByCoord.out.bam		ENCORE2	16494
DDX47_BGHLV22-10B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1533					GRCh38	V40	DDX47_BGHLV22-10B/Aligned.sortedByCoord.out.bam		ENCORE2	16534
DDX47_BGHLV22-10B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1533					GRCh38	V40	DDX47_BGHLV22-10B/Aligned.sortedByCoord.out.bam		ENCORE2	16574
DDX47_BGHLV22-10B_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1533					GRCh38	V40	DDX47_BGHLV22-10B_CGATGT_L005_001.R1.fastq.gz,DDX47_BGHLV22-10B_CGATGT_L005_001.R2.fastq.gz		ENCORE2	16614