DDX55 RNA-Seq in K562

General Information


RBP	DDX55
Cell_Line	K562
Method	shRNA
Exp_Name	DDX55-BGKLV19-K562
ENCODE_series_ID
Batch_ID	BGKLV19
Pool ID	Pool-141015
Local_Set_Name	set19
ENCODE_KD_Exp_ID	ENCSR331DUD
ENCODE_CN_Exp_ID	ENCSR661HEL
Rep1	DDX55_BGKLV19_19B
Rep2	DDX55_BGKLV19_20B
CN1	NT_BGKLV19_1B
CN2	NT_BGKLV19_2B
Rep1_qPCR	49.0
Rep2_qPCR	46.1
Rep1_WB
Rep2_WB
Antibody Cat#	A303-027A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB812HQG
Status	Archived
Project	ENCODE3
ID	469

Experiment Information (Status: Released)

	BGKLV19-19	BGKLV19-20
idx	226	227
TRCN#_or_BGC#	TRCN0000051219	TRCN0000051219
shRNA_or_gRNA_sequence	CGCAATCATAAGCAGGAGAAA	CGCAATCATAAGCAGGAGAAA
PAM
Name	DDX55	DDX55
Sample_ID	BGKLV19-19	BGKLV19-20
transduction_Date	9/4/2014	9/4/2014
days
RBP_name	DDX55	DDX55
qPCR_result	49.0	46.1
Ave_qPCR	47.6
RT-qPCR_primer-F	cgggtctcagtgaaggagaa
RT-qPCR_primer-R	ctcatctgccttgcatacca
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A303-027A	A303-027A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	12.8272785	0
Rep2_TPM	9.60551378	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	245	246

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV19-19	BGKLV19-20
Sample_ID	BGKLV19-19	BGKLV19-20
Sample Name	DDX55_BGKLV19_19B	DDX55_BGKLV19_20B
Sample Name	DDX55_BGKLV19_19B	DDX55_BGKLV19_20B
RBP	DDX55	DDX55
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	668	669

Library-Prep
Sequencing

Library-Prep Information

	BGKLV19-19	BGKLV19-20
Sample #
Sample Name	DDX55-BGKLV19-19B	DDX55-BGKLV19-20B
Sample_Name_Alias	DDX55_BGKLV19_19B	DDX55_BGKLV19_20B
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-03	2014-10-03
Lib_ID	Lib-141003	Lib-141003
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/A8.png	DNA_Library_LV18-19/set1/B8.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/E2.png	RNA_Library_LV19-21-24/set1/F2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV19-19	BGKLV19-20
RBP	DDX55	DDX55
Batch_ID	BGKLV19	BGKLV19
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2354	2355

Sequencing Information

	BGKLV19-19	BGKLV19-20
Sample_ID	BGKLV19-19	BGKLV19-20
Sample Name	DDX55_BGKLV19_19B	DDX55_BGKLV19_20B
Pool ID	Pool-141015	Pool-141015
LocalServer_folder	set19	set19
total_reads	32,700,000	44,060,000
total_aligned_reads	30,478,484	40,751,360
unique_aligned_reads	27,979,242	37,369,776
percent_uniqueAligned	0.85563	0.84816
correlation_replicates	0.996506	0.996506
spikein_reads	132,474	98,492
percent_spikeins	0.00405	0.00224
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	996	997

Data Submission Information

	BGKLV19-19
ENCODE_alias	brenton-graveley:DDX55_BGKLV19
ENCODE_accession	ENCSR331DUD
object_type	experiment
assay_type	knockdown followed by RNA-seq
Sample_ID	BGKLV19-19
Sample Name	DDX55_BGKLV19_19B
Selected	Yes
Status	Released
Status_Date	2014-12-05
Project	ENCODE3

protocol_URL
ID	2883

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
DDX55_BGKLV19_19B_GATCAG_L003_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	996	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15108
DDX55_BGKLV19_19B_GATCAG_L003_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	996	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15166
DDX55_BGKLV19_19B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	996					GRCh38	V40	DDX55_BGKLV19_19B_GATCAG_L003_R1_001.fastq.gz,DDX55_BGKLV19_19B_GATCAG_L003_R2_001.fastq.gz		ENCORE2	15224
DDX55_BGKLV19_19B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	996					GRCh38	V40	DDX55_BGKLV19_19B/Aligned.sortedByCoord.out.bam		ENCORE2	15295
DDX55_BGKLV19_19B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	996					GRCh38	V40	DDX55_BGKLV19_19B/Aligned.sortedByCoord.out.bam		ENCORE2	15353
DDX55_BGKLV19_19B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	996					GRCh38	V40	DDX55_BGKLV19_19B/Aligned.sortedByCoord.out.bam		ENCORE2	15411
DDX55_BGKLV19_19B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	996					GRCh38	V40	DDX55_BGKLV19_19B/Aligned.sortedByCoord.out.bam		ENCORE2	15469
DDX55_BGKLV19_19B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	996					GRCh38	V40	DDX55_BGKLV19_19B_GATCAG_L003_R1_001.fastq.gz,DDX55_BGKLV19_19B_GATCAG_L003_R2_001.fastq.gz		ENCORE2	16366
DDX55_BGKLV19_20B_TAGCTT_L003_R1_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	997	HiSeq2000	100	paired-ended	1				NT_BGKLV19_1B_ATCACG_L002_R1_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R1_001.fastq.gz	ENCODE3	15109
DDX55_BGKLV19_20B_TAGCTT_L003_R2_001.fastq.gz	ENCODE_DATA/set19/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	997	HiSeq2000	100	paired-ended	2				NT_BGKLV19_1B_ATCACG_L002_R2_001.fastq.gz,NT_BGKLV19_2B_CGATGT_L002_R2_001.fastq.gz	ENCODE3	15167
DDX55_BGKLV19_20B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	997					GRCh38	V40	DDX55_BGKLV19_20B_TAGCTT_L003_R1_001.fastq.gz,DDX55_BGKLV19_20B_TAGCTT_L003_R2_001.fastq.gz		ENCORE2	15225
DDX55_BGKLV19_20B_Signal.Unique.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	997					GRCh38	V40	DDX55_BGKLV19_20B/Aligned.sortedByCoord.out.bam		ENCORE2	15296
DDX55_BGKLV19_20B_Signal.Unique.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	997					GRCh38	V40	DDX55_BGKLV19_20B/Aligned.sortedByCoord.out.bam		ENCORE2	15354
DDX55_BGKLV19_20B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	997					GRCh38	V40	DDX55_BGKLV19_20B/Aligned.sortedByCoord.out.bam		ENCORE2	15412
DDX55_BGKLV19_20B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set19/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	997					GRCh38	V40	DDX55_BGKLV19_20B/Aligned.sortedByCoord.out.bam		ENCORE2	15470
DDX55_BGKLV19_20B_quant.sf	ENCODE_DATA/set19/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	997					GRCh38	V40	DDX55_BGKLV19_20B_TAGCTT_L003_R1_001.fastq.gz,DDX55_BGKLV19_20B_TAGCTT_L003_R2_001.fastq.gz		ENCORE2	16367