DDX47 RNA-Seq in K562

General Information


RBP	DDX47
Cell_Line	K562
Method	shRNA
Exp_Name	DDX47-BGKLV25-K562
ENCODE_series_ID	ENCSR253WFB
Batch_ID	BGKLV25
Pool ID	Pool-160425
Local_Set_Name	set25
ENCODE_KD_Exp_ID	ENCSR155EZL
ENCODE_CN_Exp_ID	ENCSR031RRO
Rep1	DDX47_BGKLV25-13B
Rep2	DDX47_BGKLV25-14B
CN1	NT_BGKLV25-1B
CN2	NT_BGKLV25-2B
Rep1_qPCR	45.5
Rep2_qPCR	44.3
Rep1_WB	88.7
Rep2_WB	97.0
Antibody Cat#	GTX120497
Antibody Lot#	GTX120497
Antibody DCC ID	ENCAB996IKB
Status	Released
Project	ENCODE3
ID	628

Experiment Information (Status: Released)

	BGKLV25-13	BGKLV25-14
idx	414	415
TRCN#_or_BGC#	TRCN0000005618	TRCN0000005618
shRNA_or_gRNA_sequence	CGAGTTCTGCTGTTCTGTAAA	CGAGTTCTGCTGTTCTGTAAA
PAM
Name	DDX47	DDX47
Sample_ID	BGKLV25-13	BGKLV25-14
transduction_Date	3/17/2015	3/17/2015
days
RBP_name	DDX47	DDX47
qPCR_result	45.5	44.3
Ave_qPCR	44.9
RT-qPCR_primer-F	ACAGAACGCGTCGCTGAAG
RT-qPCR_primer-R	TATCTCCAGCATCCTCTCGC
protein_conc	2521	3392
WB_result	88.7	97.0
Ave_WB	92.8
WB_DONE_date	10/20/2015
MW	51kDa
IP	1	1
antibody_Cat#	GTX120497	GTX120497
Antibody DCC ID	ENCAB996IKB	ENCAB996IKB
submitted_to_DCC_date	3/8/2016
Rep1_TPM	13.6012962	0
Rep2_TPM	6.87646944	0
Action
Library_start_date	03/04/16	03/04/16
repeat_library
Note
ID	473	474

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

Experiment Status

	BGKLV25-13	BGKLV25-14
Sample_ID	BGKLV25-13	BGKLV25-14
Sample Name	DDX47_BGKLV25-13B	DDX47_BGKLV25-14B
Sample Name	DDX47_BGKLV25-13B	DDX47_BGKLV25-14B
RBP	DDX47	DDX47
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1197	1198

Library-Prep
Sequencing

Library-Prep Information

	BGKLV25-13	BGKLV25-14
Sample #
Sample Name	DDX47-BGKLV25-13B	DDX47-BGKLV25-14B
Sample_Name_Alias	DDX47_BGKLV25-13B	DDX47_BGKLV25-14B
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-04	2016-03-04
Lib_ID	Lib-160304	Lib-160304
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set2/F1.png	DNA_Library_LV33-34-25B-32/set1/F5.png
RIN	9.1	9.0
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/A10.png	RNA_Library_LV22-23-25/set1/B10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV25-13	BGKLV25-14
RBP	DDX47	DDX47
Batch_ID	BGKLV25	BGKLV25
WB_result	88.700	97.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2896	2897

Sequencing Information

	BGKLV25-13	BGKLV25-14
Sample_ID	BGKLV25-13	BGKLV25-14
Sample Name	DDX47_BGKLV25-13B	DDX47_BGKLV25-14B
Pool ID	Pool-160425	Pool-160425
LocalServer_folder	set25	set25
total_reads	100,591,148	80,491,426
total_aligned_reads	76,605,150	61,367,696
unique_aligned_reads	70,003,848	56,176,848
percent_uniqueAligned	0.69592	0.69792
correlation_replicates	0.998437	0.998437
spikein_reads	227,892	185,462
percent_spikeins	0.00227	0.00230
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1545	1546

Data Submission Information

	BGKLV25-13	BGKLV25-13
ENCODE_alias	brenton-graveley:DDX47_BGKLV25	brenton-graveley:DDX47-BGKLV25-K562
ENCODE_accession	ENCSR155EZL	ENCSR253WFB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV25-13	BGKLV25-13
Sample Name	DDX47_BGKLV25-13B	DDX47_BGKLV25-13B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-05-25	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3138	6654

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_BGKLV25-13B_ACAGTG_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1545	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1B_ATCACG_L008_001.R1.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R1.fastq.gz	ENCODE3	19568
DDX47_BGKLV25-13B_ACAGTG_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1545	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1B_ATCACG_L008_001.R2.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R2.fastq.gz	ENCODE3	19604
DDX47_BGKLV25-13B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1545					GRCh38	V40	DDX47_BGKLV25-13B_ACAGTG_L008_001.R1.fastq.gz,DDX47_BGKLV25-13B_ACAGTG_L008_001.R2.fastq.gz		ENCORE2	19640
DDX47_BGKLV25-13B_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1545					GRCh38	V40	DDX47_BGKLV25-13B/Aligned.sortedByCoord.out.bam		ENCORE2	19676
DDX47_BGKLV25-13B_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1545					GRCh38	V40	DDX47_BGKLV25-13B/Aligned.sortedByCoord.out.bam		ENCORE2	19712
DDX47_BGKLV25-13B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1545					GRCh38	V40	DDX47_BGKLV25-13B/Aligned.sortedByCoord.out.bam		ENCORE2	19748
DDX47_BGKLV25-13B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1545					GRCh38	V40	DDX47_BGKLV25-13B/Aligned.sortedByCoord.out.bam		ENCORE2	19784
DDX47_BGKLV25-13B_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1545					GRCh38	V40	DDX47_BGKLV25-13B_ACAGTG_L008_001.R1.fastq.gz,DDX47_BGKLV25-13B_ACAGTG_L008_001.R2.fastq.gz		ENCORE2	19974
DDX47_BGKLV25-14B_GCCAAT_L008_001.R1.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1546	HiSeq2000	100	paired-ended	1				NT_BGKLV25-1B_ATCACG_L008_001.R1.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R1.fastq.gz	ENCODE3	19569
DDX47_BGKLV25-14B_GCCAAT_L008_001.R2.fastq.gz	ENCODE_DATA/set25/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1546	HiSeq2000	100	paired-ended	2				NT_BGKLV25-1B_ATCACG_L008_001.R2.fastq.gz,NT_BGKLV25-2B_CGATGT_L008_001.R2.fastq.gz	ENCODE3	19605
DDX47_BGKLV25-14B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1546					GRCh38	V40	DDX47_BGKLV25-14B_GCCAAT_L008_001.R1.fastq.gz,DDX47_BGKLV25-14B_GCCAAT_L008_001.R2.fastq.gz		ENCORE2	19641
DDX47_BGKLV25-14B_Signal.Unique.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1546					GRCh38	V40	DDX47_BGKLV25-14B/Aligned.sortedByCoord.out.bam		ENCORE2	19677
DDX47_BGKLV25-14B_Signal.Unique.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1546					GRCh38	V40	DDX47_BGKLV25-14B/Aligned.sortedByCoord.out.bam		ENCORE2	19713
DDX47_BGKLV25-14B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1546					GRCh38	V40	DDX47_BGKLV25-14B/Aligned.sortedByCoord.out.bam		ENCORE2	19749
DDX47_BGKLV25-14B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set25/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1546					GRCh38	V40	DDX47_BGKLV25-14B/Aligned.sortedByCoord.out.bam		ENCORE2	19785
DDX47_BGKLV25-14B_quant.sf	ENCODE_DATA/set25/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1546					GRCh38	V40	DDX47_BGKLV25-14B_GCCAAT_L008_001.R1.fastq.gz,DDX47_BGKLV25-14B_GCCAAT_L008_001.R2.fastq.gz		ENCORE2	19975