DDX59 RNA-Seq in K562

Experiment Information (Status: NotSatisfied)

	BGKLV36-13	BGKLV36-14
idx	736	737
TRCN#_or_BGC#	TRCN0000050911	TRCN0000050911
shRNA_or_gRNA_sequence	CCACAGCTTTATCGTCTGCAA	CCACAGCTTTATCGTCTGCAA
PAM
Name	DDX59	DDX59
Sample_ID	BGKLV36-13	BGKLV36-14
transduction_Date	5/19/2016	5/19/2016
days
RBP_name	DDX59	DDX59
qPCR_result	51.6	52.5
Ave_qPCR	52.1
RT-qPCR_primer-F	ctctgtggtgtaaagattgtgg
RT-qPCR_primer-R	caagcacttgttgttgaaaacc
protein_conc	4602	4961
WB_result	38.9	37.6
Ave_WB	38.3
WB_DONE_date	6/15/16	wes
MW	69kDa
IP
antibody_Cat#	303-028A	303-028A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	4.1	0
Rep2_TPM	5.3	0
Action
Library_start_date	12/19/17	12/19/17
repeat_library
Note
ID	827	828

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV36-13	BGKLV36-14
Sample_ID	BGKLV36-13	BGKLV36-14
Sample Name	DDX59-BGKLV36-13C	DDX59-BGKLV36-14C
Sample Name
RBP	DDX59	DDX59
Cell_Line	K562	K562
Exp UID
Status	NotSatisfied	NotSatisfied
Status_date	2020-11-04	2020-11-04
Project	ENCODE4	ENCODE4
Note	bad KD%	bad KD%
ID	6463	6464

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-13	BGKLV36-14
Sample #	47	48
Sample Name	DDX59-BGKLV36-13C	DDX59-BGKLV36-14C
Sample_Name_Alias
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	362	292
Peak_Molarity	10.60	10.10
libSampleQC_DNA_Well	DNA_Library_set40/set1/G11.png	DNA_Library_set40/set1/H11.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set40/set1/C6.png	RNA_Library_set40/set1/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGKLV36-13	BGKLV36-14
RBP	DDX59	DDX59
Batch_ID	BGKLV36	BGKLV36
WB_result	38.900	37.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	970	971

Sequencing Information

	BGKLV36-13	BGKLV36-14
Sample_ID	BGKLV36-13	BGKLV36-14
Sample Name	DDX59-BGKLV36-13C	DDX59-BGKLV36-14C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_K	set40_K
total_reads	52,190,414	57,202,868
total_aligned_reads	46,833,670	50,413,768
unique_aligned_reads	42,958,574	46,189,418
percent_uniqueAligned	0.82311	0.80747
correlation_replicates	0.998821	0.998821
spikein_reads	11,196	11,242
percent_spikeins	0.00021	0.00020
original_ReadLength	100	100
QC_Status	OtherReasonsNotToSubmit	OtherReasonsNotToSubmit
ID	373	374

Data Submission Information DCC submission information was not avaliable

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
DDX59-BGKLV36-13C_CAGATC_ACBYWVANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	373	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1C_L001_001.R1.fastq.gz,NT-BGKLV36-2C_L001_001.R1.fastq.gz	ENCODE4	723
DDX59-BGKLV36-13C_CAGATC_ACBYWVANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	373	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1C_L001_001.R2.fastq.gz,NT-BGKLV36-2C_L001_001.R2.fastq.gz	ENCODE4	766
DDX59-BGKLV36-13C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	373					GRCh38	V40	DDX59-BGKLV36-13C_CAGATC_ACBYWVANXX_L007_001.R1.fastq.gz,DDX59-BGKLV36-13C_CAGATC_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23470
DDX59-BGKLV36-13C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	373					GRCh38	V40	DDX59-BGKLV36-13C/Aligned.sortedByCoord.out.bam		ENCORE2	23504
DDX59-BGKLV36-13C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	373					GRCh38	V40	DDX59-BGKLV36-13C/Aligned.sortedByCoord.out.bam		ENCORE2	23538
DDX59-BGKLV36-13C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	373					GRCh38	V40	DDX59-BGKLV36-13C/Aligned.sortedByCoord.out.bam		ENCORE2	23572
DDX59-BGKLV36-13C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	373					GRCh38	V40	DDX59-BGKLV36-13C/Aligned.sortedByCoord.out.bam		ENCORE2	23606
DDX59-BGKLV36-13C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	373					GRCh38	V40	DDX59-BGKLV36-13C_CAGATC_ACBYWVANXX_L007_001.R1.fastq.gz,DDX59-BGKLV36-13C_CAGATC_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23640
DDX59-BGKLV36-14C_ACTTGA_ACBYWVANXX_L007_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	374	HiSeq2500	100	paired-ended	1				NT-BGKLV36-1C_L001_001.R1.fastq.gz,NT-BGKLV36-2C_L001_001.R1.fastq.gz	ENCODE4	724
DDX59-BGKLV36-14C_ACTTGA_ACBYWVANXX_L007_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	374	HiSeq2500	100	paired-ended	2				NT-BGKLV36-1C_L001_001.R2.fastq.gz,NT-BGKLV36-2C_L001_001.R2.fastq.gz	ENCODE4	767
DDX59-BGKLV36-14C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	374					GRCh38	V40	DDX59-BGKLV36-14C_ACTTGA_ACBYWVANXX_L007_001.R1.fastq.gz,DDX59-BGKLV36-14C_ACTTGA_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23471
DDX59-BGKLV36-14C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	374					GRCh38	V40	DDX59-BGKLV36-14C/Aligned.sortedByCoord.out.bam		ENCORE2	23505
DDX59-BGKLV36-14C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	374					GRCh38	V40	DDX59-BGKLV36-14C/Aligned.sortedByCoord.out.bam		ENCORE2	23539
DDX59-BGKLV36-14C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	374					GRCh38	V40	DDX59-BGKLV36-14C/Aligned.sortedByCoord.out.bam		ENCORE2	23573
DDX59-BGKLV36-14C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	374					GRCh38	V40	DDX59-BGKLV36-14C/Aligned.sortedByCoord.out.bam		ENCORE2	23607
DDX59-BGKLV36-14C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	374					GRCh38	V40	DDX59-BGKLV36-14C_ACTTGA_ACBYWVANXX_L007_001.R1.fastq.gz,DDX59-BGKLV36-14C_ACTTGA_ACBYWVANXX_L007_001.R2.fastq.gz		ENCORE2	23641