DDX55 RNA-Seq in K562

General Information


RBP	DDX55
Cell_Line	K562
Method	shRNA
Exp_Name	DDX55-BGKLV21-K562
ENCODE_series_ID	ENCSR782WSH
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR856CJK
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	DDX55_BGKLV21_7_17560
Rep2	DDX55_BGKLV21_8_17561
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	63.3
Rep2_qPCR	50.9
Rep1_WB	60.1
Rep2_WB	44.5
Antibody Cat#	A303-027A
Antibody Lot#	A303-027A
Antibody DCC ID	ENCAB812HQG
Status	Released
Project	ENCODE3
ID	507

Experiment Information (Status: Released)

	BGKLV21-7	BGKLV21-8
idx	278	279
TRCN#_or_BGC#	TRCN0000051219	TRCN0000051219
shRNA_or_gRNA_sequence	CGCAATCATAAGCAGGAGAAA	CGCAATCATAAGCAGGAGAAA
PAM
Name	DDX55	DDX55
Sample_ID	BGKLV21-7	BGKLV21-8
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	DDX55	DDX55
qPCR_result	63.3	50.9
Ave_qPCR	57.1
RT-qPCR_primer-F	cgggtctcagtgaaggagaa
RT-qPCR_primer-R	ctcatctgccttgcatacca
protein_conc	3718	3807
WB_result	60.1	44.5
Ave_WB	52.3
WB_DONE_date	2/13/2015
MW
IP	1	1
antibody_Cat#	A303-027A	A303-027A
Antibody DCC ID	ENCAB812HQG	ENCAB812HQG
submitted_to_DCC_date	5/4/2015
Rep1_TPM	12.8272785	0
Rep2_TPM	9.60551378	0
Action
Library_start_date	5/19/2015	5/19/2015
repeat_library
Note
ID	303	304

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX55	Product_ID: A303-027A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX55-human

Experiment Status

	BGKLV21-7	BGKLV21-8
Sample_ID	BGKLV21-7	BGKLV21-8
Sample Name	DDX55_BGKLV21_7_17560	DDX55_BGKLV21_8_17561
Sample Name	DDX55_BGKLV21_7_17560	DDX55_BGKLV21_8_17561
RBP	DDX55	DDX55
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	746	747

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-7	BGKLV21-8
Sample #
Sample Name	DDX55-BGKLV21-7	DDX55-BGKLV21-8
Sample_Name_Alias	DDX55_BGKLV21_7_17560	DDX55_BGKLV21_8_17561
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/E5.png	DNA_Library_LV21-24/set1/F5.png
RIN	9.7	10.0
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/G7.png	RNA_Library_LV19-21-24/set2/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-7	BGKLV21-8
RBP	DDX55	DDX55
Batch_ID	BGKLV21	BGKLV21
WB_result	60.100	44.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2432	2433

Sequencing Information

	BGKLV21-7	BGKLV21-8
Sample_ID	BGKLV21-7	BGKLV21-8
Sample Name	DDX55_BGKLV21_7_17560	DDX55_BGKLV21_8_17561
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	33,770,000	46,870,000
total_aligned_reads	29,953,066	40,491,934
unique_aligned_reads	27,344,620	36,917,740
percent_uniqueAligned	0.80973	0.78766
correlation_replicates	0.998457	0.998457
spikein_reads	186,624	249,794
percent_spikeins	0.00553	0.00533
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1038	1039

Data Submission Information

	BGKLV21-7	BGKLV21-7
ENCODE_alias	brenton-graveley:DDX55_BGKLV21	brenton-graveley:DDX55-BGKLV21-K562
ENCODE_accession	ENCSR856CJK	ENCSR782WSH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-7	BGKLV21-7
Sample Name	DDX55_BGKLV21_7_17560	DDX55_BGKLV21_7_17560
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2959	6660

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_BGKLV21_7_17560_ACAGTG_L001_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1038	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15922
DDX55_BGKLV21_7_17560_ACAGTG_L001_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1038	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15966
DDX55_BGKLV21_7_17560_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1038					GRCh38	V40	DDX55_BGKLV21_7_17560_ACAGTG_L001_R1_001.fastq.gz,DDX55_BGKLV21_7_17560_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	16010
DDX55_BGKLV21_7_17560_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1038					GRCh38	V40	DDX55_BGKLV21_7_17560/Aligned.sortedByCoord.out.bam		ENCORE2	16054
DDX55_BGKLV21_7_17560_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1038					GRCh38	V40	DDX55_BGKLV21_7_17560/Aligned.sortedByCoord.out.bam		ENCORE2	16098
DDX55_BGKLV21_7_17560_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1038					GRCh38	V40	DDX55_BGKLV21_7_17560/Aligned.sortedByCoord.out.bam		ENCORE2	16142
DDX55_BGKLV21_7_17560_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1038					GRCh38	V40	DDX55_BGKLV21_7_17560/Aligned.sortedByCoord.out.bam		ENCORE2	16186
DDX55_BGKLV21_7_17560_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1038					GRCh38	V40	DDX55_BGKLV21_7_17560_ACAGTG_L001_R1_001.fastq.gz,DDX55_BGKLV21_7_17560_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	16230
DDX55_BGKLV21_8_17561_GCCAAT_L001_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1039	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15923
DDX55_BGKLV21_8_17561_GCCAAT_L001_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1039	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15967
DDX55_BGKLV21_8_17561_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1039					GRCh38	V40	DDX55_BGKLV21_8_17561_GCCAAT_L001_R1_001.fastq.gz,DDX55_BGKLV21_8_17561_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	16011
DDX55_BGKLV21_8_17561_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1039					GRCh38	V40	DDX55_BGKLV21_8_17561/Aligned.sortedByCoord.out.bam		ENCORE2	16055
DDX55_BGKLV21_8_17561_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1039					GRCh38	V40	DDX55_BGKLV21_8_17561/Aligned.sortedByCoord.out.bam		ENCORE2	16099
DDX55_BGKLV21_8_17561_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1039					GRCh38	V40	DDX55_BGKLV21_8_17561/Aligned.sortedByCoord.out.bam		ENCORE2	16143
DDX55_BGKLV21_8_17561_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1039					GRCh38	V40	DDX55_BGKLV21_8_17561/Aligned.sortedByCoord.out.bam		ENCORE2	16187
DDX55_BGKLV21_8_17561_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1039					GRCh38	V40	DDX55_BGKLV21_8_17561_GCCAAT_L001_R1_001.fastq.gz,DDX55_BGKLV21_8_17561_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	16231