DDX24 RNA-Seq in K562

General Information


RBP	DDX24
Cell_Line	K562
Method	shRNA
Exp_Name	DDX24-BGKLV08-K562
ENCODE_series_ID	ENCSR684FWZ
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR067LLB
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	DDX24-LV08-13
Rep2	DDX24-LV08-14
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	85.4
Rep2_qPCR	80.4
Rep1_WB	79.4
Rep2_WB	51.9
Antibody Cat#	A300-696A
Antibody Lot#	A300-696A
Antibody DCC ID	ENCAB988AYG
Status	Released
Project	ENCODE3
ID	283

Experiment Information (Status: Released)

	BGKLV08-13	BGKLV08-14
idx	14	15
TRCN#_or_BGC#	TRCN0000050314	TRCN0000050314
shRNA_or_gRNA_sequence	CGCTCAAGAAAGATGAGGATA	CGCTCAAGAAAGATGAGGATA
PAM
Name	DDX24	DDX24
Sample_ID	BGKLV08-13	BGKLV08-14
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	DDX24	DDX24
qPCR_result	85.4	80.4
Ave_qPCR	82.9
RT-qPCR_primer-F	AACTCTTGGATTGAGCAGGC
RT-qPCR_primer-R	GTCTCCGACGTTCTTCTTGC
protein_conc	2976	2728
WB_result	79.4	51.9
Ave_WB	65.7
WB_DONE_date	7/24/2015
MW	96kDa
IP	1	1
antibody_Cat#	A300-696A	A300-696A
Antibody DCC ID	ENCAB988AYG	ENCAB988AYG
submitted_to_DCC_date	8/6/2015
Rep1_TPM	52.8661833	0
Rep2_TPM	36.5986354	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note
ID	13	14

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX24	Product_ID: A300-696A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX24-human

Experiment Status

	BGKLV08-13	BGKLV08-14
Sample_ID	BGKLV08-13	BGKLV08-14
Sample Name	DDX24-LV08-13	DDX24-LV08-14
Sample Name	DDX24-LV08-13	DDX24-LV08-14
RBP	DDX24	DDX24
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	274	275

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-13	BGKLV08-14
Sample #
Sample Name	DDX24-BGKLV08-13	DDX24-BGKLV08-14
Sample_Name_Alias	DDX24-LV08-13	DDX24-LV08-14
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-05	2014-05-05
Lib_ID	Lib-140505	Lib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set1/B2.png	DNA_Library_LV08/set1/C2.png
RIN	9.5	9.3
libSample_RNA_Well	RNA_Library_LV08/set1/E2.png	RNA_Library_LV08/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-13	BGKLV08-14
RBP	DDX24	DDX24
Batch_ID	BGKLV08	BGKLV08
WB_result	79.400	51.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1896	1897

Sequencing Information

	BGKLV08-13	BGKLV08-14
Sample_ID	BGKLV08-13	BGKLV08-14
Sample Name	DDX24-LV08-13	DDX24-LV08-14
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	57,760,000	55,570,000
total_aligned_reads	51,158,214	48,615,338
unique_aligned_reads	46,771,794	44,394,048
percent_uniqueAligned	0.80976	0.79889
correlation_replicates	0.998559	0.998559
spikein_reads	411,096	445,504
percent_spikeins	0.00712	0.00802
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	596	597

Data Submission Information

	BGKLV08-13	BGKLV08-13
ENCODE_alias	brenton-graveley:DDX24-LV08	brenton-graveley:DDX24-BGKLV08-K562
ENCODE_accession	ENCSR067LLB	ENCSR684FWZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-13	BGKLV08-13
Sample Name	DDX24-LV08-13	DDX24-LV08-13
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2686	6646

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
DDX24-LV08-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	596					GRCh38	V40	DDX24-LV08-13_GATCAG_L002_R1_001.fastq.gz,DDX24-LV08-13_GATCAG_L002_R2_001.fastq.gz		ENCORE2	11981
DDX24-LV08-13_GATCAG_L002_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	596	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12037
DDX24-LV08-13_GATCAG_L002_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	596	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12093
DDX24-LV08-13_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	596					GRCh38	V40	DDX24-LV08-13/Aligned.sortedByCoord.out.bam		ENCORE2	12149
DDX24-LV08-13_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	596					GRCh38	V40	DDX24-LV08-13/Aligned.sortedByCoord.out.bam		ENCORE2	12205
DDX24-LV08-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	596					GRCh38	V40	DDX24-LV08-13/Aligned.sortedByCoord.out.bam		ENCORE2	12261
DDX24-LV08-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	596					GRCh38	V40	DDX24-LV08-13/Aligned.sortedByCoord.out.bam		ENCORE2	12317
DDX24-LV08-13_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	596					GRCh38	V40	DDX24-LV08-13_GATCAG_L002_R1_001.fastq.gz,DDX24-LV08-13_GATCAG_L002_R2_001.fastq.gz		ENCORE2	13316
DDX24-LV08-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	597					GRCh38	V40	DDX24-LV08-14_TAGCTT_L002_R1_001.fastq.gz,DDX24-LV08-14_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	11982
DDX24-LV08-14_TAGCTT_L002_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	597	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12038
DDX24-LV08-14_TAGCTT_L002_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	597	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12094
DDX24-LV08-14_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	597					GRCh38	V40	DDX24-LV08-14/Aligned.sortedByCoord.out.bam		ENCORE2	12150
DDX24-LV08-14_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	597					GRCh38	V40	DDX24-LV08-14/Aligned.sortedByCoord.out.bam		ENCORE2	12206
DDX24-LV08-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	597					GRCh38	V40	DDX24-LV08-14/Aligned.sortedByCoord.out.bam		ENCORE2	12262
DDX24-LV08-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	597					GRCh38	V40	DDX24-LV08-14/Aligned.sortedByCoord.out.bam		ENCORE2	12318
DDX24-LV08-14_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	597					GRCh38	V40	DDX24-LV08-14_TAGCTT_L002_R1_001.fastq.gz,DDX24-LV08-14_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	13317