DDX21 RNA-Seq in K562

General Information


RBP	DDX21
Cell_Line	K562
Method	shRNA
Exp_Name	DDX21-BGKLV11-K562
ENCODE_series_ID	ENCSR557DHX
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR961WVL
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	DDX21-LV11-9
Rep2	DDX21-LV11-10
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	85.3
Rep2_qPCR	89.1
Rep1_WB	90.9
Rep2_WB	86.2
Antibody Cat#	RN090PW
Antibody Lot#	RN090PW
Antibody DCC ID	ENCAB315FWL
Status	Archived
Project	ENCODE3
ID	307

Experiment Information (Status: Released)

	BGKLV11-9	BGKLV11-10
idx	78	79
TRCN#_or_BGC#	TRCN0000051198	TRCN0000051198
shRNA_or_gRNA_sequence	GCGGAGTTTCAGTAAAGCATT	GCGGAGTTTCAGTAAAGCATT
PAM
Name	DDX21	DDX21
Sample_ID	BGKLV11-9	BGKLV11-10
transduction_Date	5/1/2014	5/1/2014
days
RBP_name	DDX21	DDX21
qPCR_result	85.3	89.1
Ave_qPCR	87.2
RT-qPCR_primer-F	TTGCTTTGATGTACCTACCGC
RT-qPCR_primer-R	AGTTCTGGTTGCTCTGTGGC
protein_conc	1775	1448
WB_result	90.9	86.2
Ave_WB	88.6
WB_DONE_date	6/24/2015
MW	87kDa
IP	1	1
antibody_Cat#	RN090PW	RN090PW
Antibody DCC ID	ENCAB315FWL	ENCAB315FWL
submitted_to_DCC_date	8/6/2015
Rep1_TPM	228.755215	0
Rep2_TPM	130.685965	0
Action	Ready	Ready
Library_start_date	5/19/2014	5/19/2014
repeat_library
Note
ID	83	84

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX21	Product_ID: RN090PW Lot_ID: 1 Source: MBLI Target Name: DDX21-human

Experiment Status

	BGKLV11-9	BGKLV11-10
Sample_ID	BGKLV11-9	BGKLV11-10
Sample Name	DDX21-LV11-9	DDX21-LV11-10
Sample Name	DDX21-LV11-9	DDX21-LV11-10
RBP	DDX21	DDX21
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	327	326

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-9	BGKLV11-10
Sample #
Sample Name	DDX21-BGKLV11-9	DDX21-BGKLV11-10
Sample_Name_Alias	DDX21-LV11-9	DDX21-LV11-10
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-19	2014-05-19
Lib_ID	Lib-140519	Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV11/set1/F1.png	DNA_Library_LV11/set1/G1.png
RIN	9.1	9.4
libSample_RNA_Well	RNA_Library_LV11/set1/E1.png	RNA_Library_LV11/set1/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-9	BGKLV11-10
RBP	DDX21	DDX21
Batch_ID	BGKLV11	BGKLV11
WB_result	90.900	86.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1949	1948

Sequencing Information

	BGKLV11-9	BGKLV11-10
Sample_ID	BGKLV11-9	BGKLV11-10
Sample Name	DDX21-LV11-9	DDX21-LV11-10
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	72,860,000	64,480,000
total_aligned_reads	57,548,034	52,905,236
unique_aligned_reads	52,742,608	48,161,720
percent_uniqueAligned	0.72389	0.74692
correlation_replicates	0.991202	0.991202
spikein_reads	439,962	473,408
percent_spikeins	0.00604	0.00734
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	649	648

Data Submission Information

	BGKLV11-9	BGKLV11-9
ENCODE_alias	brenton-graveley:DDX21-LV11	brenton-graveley:DDX21-BGKLV11-K562
ENCODE_accession	ENCSR961WVL	ENCSR557DHX
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-9	BGKLV11-9
Sample Name	DDX21-LV11-9	DDX21-LV11-9
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2712	6644

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
DDX21-LV11-9_ACAGTG_L001_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	649	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12370
DDX21-LV11-9_ACAGTG_L001_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	649	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12418
DDX21-LV11-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	649					GRCh38	V40	DDX21-LV11-9_ACAGTG_L001_R1_001.fastq.gz,DDX21-LV11-9_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	12466
DDX21-LV11-9_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	649					GRCh38	V40	DDX21-LV11-9/Aligned.sortedByCoord.out.bam		ENCORE2	12514
DDX21-LV11-9_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	649					GRCh38	V40	DDX21-LV11-9/Aligned.sortedByCoord.out.bam		ENCORE2	12562
DDX21-LV11-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	649					GRCh38	V40	DDX21-LV11-9/Aligned.sortedByCoord.out.bam		ENCORE2	12610
DDX21-LV11-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	649					GRCh38	V40	DDX21-LV11-9/Aligned.sortedByCoord.out.bam		ENCORE2	12658
DDX21-LV11-9_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	649					GRCh38	V40	DDX21-LV11-9_ACAGTG_L001_R1_001.fastq.gz,DDX21-LV11-9_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	12706
DDX21-LV11-10_GCCAAT_L001_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	648	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12369
DDX21-LV11-10_GCCAAT_L001_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	648	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12417
DDX21-LV11-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	648					GRCh38	V40	DDX21-LV11-10_GCCAAT_L001_R1_001.fastq.gz,DDX21-LV11-10_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	12465
DDX21-LV11-10_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	648					GRCh38	V40	DDX21-LV11-10/Aligned.sortedByCoord.out.bam		ENCORE2	12513
DDX21-LV11-10_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	648					GRCh38	V40	DDX21-LV11-10/Aligned.sortedByCoord.out.bam		ENCORE2	12561
DDX21-LV11-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	648					GRCh38	V40	DDX21-LV11-10/Aligned.sortedByCoord.out.bam		ENCORE2	12609
DDX21-LV11-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	648					GRCh38	V40	DDX21-LV11-10/Aligned.sortedByCoord.out.bam		ENCORE2	12657
DDX21-LV11-10_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	648					GRCh38	V40	DDX21-LV11-10_GCCAAT_L001_R1_001.fastq.gz,DDX21-LV11-10_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	12705