DDX6 RNA-Seq in K562

General Information


RBP	DDX6
Cell_Line	K562
Method	shRNA
Exp_Name	DDX6-BGKLV08-K562
ENCODE_series_ID	ENCSR501LFJ
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR119QWQ
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	DDX6-LV08-17
Rep2	DDX6-LV08-18
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	67.9
Rep2_qPCR	65.9
Rep1_WB	30.3
Rep2_WB	21.4
Antibody Cat#	A300-460A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB348UON
Status	Archived
Project	ENCODE3
ID	285

Experiment Information (Status: Released)

	BGKLV08-17	BGKLV08-18
idx	18	19
TRCN#_or_BGC#	TRCN0000074696	TRCN0000074696
shRNA_or_gRNA_sequence	CTGATCTGTTTACCCGAGGTA	CTGATCTGTTTACCCGAGGTA
PAM
Name	DDX6	DDX6
Sample_ID	BGKLV08-17	BGKLV08-18
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	DDX6	DDX6
qPCR_result	67.9	65.9
Ave_qPCR	66.9
RT-qPCR_primer-F	TACCACAGCGAGCCTGTAGA
RT-qPCR_primer-R	TGTCACAGATCCAAACGAGC
protein_conc	2769	2481
WB_result	30.3	21.4
Ave_WB	25.9
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A300-460A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	10.2125759	0
Rep2_TPM	7.30947544	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note
ID	17	18

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV08-17	BGKLV08-18
Sample_ID	BGKLV08-17	BGKLV08-18
Sample Name	DDX6-LV08-17	DDX6-LV08-18
Sample Name	DDX6-LV08-17	DDX6-LV08-18
RBP	DDX6	DDX6
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	278	279

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-17	BGKLV08-18
Sample #
Sample Name	DDX6-BGKLV08-17	DDX6-BGKLV08-18
Sample_Name_Alias	DDX6-LV08-17	DDX6-LV08-18
Index Well Position	S13	S14
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/F2.png	DNA_Library_LV08/set1/G2.png
RIN	9.1	9.3
libSample_RNA_Well	RNA_Library_LV08/set2/A1.png	RNA_Library_LV08/set2/B1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-17	BGKLV08-18
RBP	DDX6	DDX6
Batch_ID	BGKLV08	BGKLV08
WB_result	30.300	21.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1900	1901

Sequencing Information

	BGKLV08-17	BGKLV08-18
Sample_ID	BGKLV08-17	BGKLV08-18
Sample Name	DDX6-LV08-17	DDX6-LV08-18
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	51,460,000	46,520,000
total_aligned_reads	43,871,264	40,232,744
unique_aligned_reads	40,110,986	36,665,128
percent_uniqueAligned	0.77946	0.78816
correlation_replicates	0.998726	0.998726
spikein_reads	456,568	400,174
percent_spikeins	0.00887	0.00860
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	600	601

Data Submission Information

	BGKLV08-17	BGKLV08-17
ENCODE_alias	brenton-graveley:DDX6-LV08	brenton-graveley:DDX6-BGKLV08-K562
ENCODE_accession	ENCSR119QWQ	ENCSR501LFJ
object_type	experiment	experiment
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-17	BGKLV08-17
Sample Name	DDX6-LV08-17	DDX6-LV08-17
Selected	Yes	No
Status	Released	Archived
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2688	6663

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
DDX6-LV08-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	600					GRCh38	V40	DDX6-LV08-17_AGTCAA_L002_R1_001.fastq.gz,DDX6-LV08-17_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	11985
DDX6-LV08-17_AGTCAA_L002_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	600	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	12041
DDX6-LV08-17_AGTCAA_L002_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	600	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	12097
DDX6-LV08-17_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	600					GRCh38	V40	DDX6-LV08-17/Aligned.sortedByCoord.out.bam		ENCORE2	12153
DDX6-LV08-17_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	600					GRCh38	V40	DDX6-LV08-17/Aligned.sortedByCoord.out.bam		ENCORE2	12209
DDX6-LV08-17_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	600					GRCh38	V40	DDX6-LV08-17/Aligned.sortedByCoord.out.bam		ENCORE2	12265
DDX6-LV08-17_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	600					GRCh38	V40	DDX6-LV08-17/Aligned.sortedByCoord.out.bam		ENCORE2	12321
DDX6-LV08-17_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	600					GRCh38	V40	DDX6-LV08-17_AGTCAA_L002_R1_001.fastq.gz,DDX6-LV08-17_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	13320
DDX6-LV08-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	601					GRCh38	V40	DDX6-LV08-18_AGTTCC_L002_R1_001.fastq.gz,DDX6-LV08-18_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	11986
DDX6-LV08-18_AGTTCC_L002_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	601	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	12042
DDX6-LV08-18_AGTTCC_L002_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	601	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	12098
DDX6-LV08-18_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	601					GRCh38	V40	DDX6-LV08-18/Aligned.sortedByCoord.out.bam		ENCORE2	12154
DDX6-LV08-18_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	601					GRCh38	V40	DDX6-LV08-18/Aligned.sortedByCoord.out.bam		ENCORE2	12210
DDX6-LV08-18_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	601					GRCh38	V40	DDX6-LV08-18/Aligned.sortedByCoord.out.bam		ENCORE2	12266
DDX6-LV08-18_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	601					GRCh38	V40	DDX6-LV08-18/Aligned.sortedByCoord.out.bam		ENCORE2	12322
DDX6-LV08-18_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	601					GRCh38	V40	DDX6-LV08-18_AGTTCC_L002_R1_001.fastq.gz,DDX6-LV08-18_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	13321