DDX55 RNA-Seq in HepG2

General Information


RBP	DDX55
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX55-BGHLV17-HepG2
ENCODE_series_ID	ENCSR145BKW
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR964YTW
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	DDX55_BGHLV17_59
Rep2	DDX55_BGHLV17_60
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	82.0
Rep2_qPCR	68.0
Rep1_WB	70.0
Rep2_WB	65.5
Antibody Cat#	A303-027A
Antibody Lot#	A303-027A
Antibody DCC ID	ENCAB812HQG
Status	Released
Project	ENCODE3
ID	432

Experiment Information (Status: Released)

	BGHLV17-59	BGHLV17-60
idx	295	296
TRCN#_or_BGC#	TRCN0000051219	TRCN0000051219
shRNA_or_gRNA_sequence	CGCAATCATAAGCAGGAGAAA	CGCAATCATAAGCAGGAGAAA
PAM
Name	DDX55	DDX55
Sample_ID	BGHLV17-59	BGHLV17-60
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	DDX55	DDX55
qPCR_result	82.0	68.0
Ave_qPCR	75.0
RT-qPCR_primer-F	cgggtctcagtgaaggagaa
RT-qPCR_primer-R	ctcatctgccttgcatacca
protein_conc	3476	2681
WB_result	70.0	65.5
Ave_WB	67.8
WB_DONE_date	4/16/2015
MW	69kDa
IP	1	1
antibody_Cat#	A303-027A	A303-027A
Antibody DCC ID	ENCAB812HQG	ENCAB812HQG
submitted_to_DCC_date	5/4/2015
Rep1_TPM	10.1	0
Rep2_TPM	8.3	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2360	2361

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

	BGHLV17-59	BGHLV17-60
Sample_ID	BGHLV17-59	BGHLV17-60
Sample Name	DDX55_BGHLV17_59	DDX55_BGHLV17_60
Sample Name	DDX55_BGHLV17_59	DDX55_BGHLV17_60
RBP	DDX55	DDX55
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	590	591

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-59	BGHLV17-60
Sample #
Sample Name	DDX55-BGHLV17-59	DDX55-BGHLV17-60
Sample_Name_Alias	DDX55_BGHLV17_59	DDX55_BGHLV17_60
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/C5.png	DNA_Library_LV16-17/set1/D5.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/C7.png	RNA_Library_LV16-17-18/set1/D7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-59	BGHLV17-60
RBP	DDX55	DDX55
Batch_ID	BGHLV17	BGHLV17
WB_result	70.000	65.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2274	2275

Sequencing Information

	BGHLV17-59	BGHLV17-60
Sample_ID	BGHLV17-59	BGHLV17-60
Sample Name	DDX55_BGHLV17_59	DDX55_BGHLV17_60
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	65,280,000	69,950,000
total_aligned_reads	58,079,984	62,527,202
unique_aligned_reads	54,818,534	59,006,546
percent_uniqueAligned	0.83974	0.84355
correlation_replicates	0.997324	0.997324
spikein_reads	253,890	165,406
percent_spikeins	0.00389	0.00236
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	916	917

Data Submission Information

	BGHLV17-59	BGHLV17-59
ENCODE_alias	brenton-graveley:DDX55_BGHLV17	brenton-graveley:DDX55-BGHLV17-HepG2
ENCODE_accession	ENCSR964YTW	ENCSR145BKW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-59	BGHLV17-59
Sample Name	DDX55_BGHLV17_59	DDX55_BGHLV17_59
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2863	6659

File Information

Search:

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_BGHLV17_59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	916					GRCh38	V40	DDX55_BGHLV17_59_GGCTAC_L005_R1_001.fastq.gz,DDX55_BGHLV17_59_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	14574
DDX55_BGHLV17_59_GGCTAC_L005_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	916	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14498
DDX55_BGHLV17_59_GGCTAC_L005_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	916	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14536
DDX55_BGHLV17_59_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	916					GRCh38	V40	DDX55_BGHLV17_59_GGCTAC_L005_R1_001.fastq.gz,DDX55_BGHLV17_59_GGCTAC_L005_R2_001.fastq.gz		ENCORE2	14764
DDX55_BGHLV17_59_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	916					GRCh38	V40	DDX55_BGHLV17_59/Aligned.sortedByCoord.out.bam		ENCORE2	14612
DDX55_BGHLV17_59_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	916					GRCh38	V40	DDX55_BGHLV17_59/Aligned.sortedByCoord.out.bam		ENCORE2	14650
DDX55_BGHLV17_59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	916					GRCh38	V40	DDX55_BGHLV17_59/Aligned.sortedByCoord.out.bam		ENCORE2	14688
DDX55_BGHLV17_59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	916					GRCh38	V40	DDX55_BGHLV17_59/Aligned.sortedByCoord.out.bam		ENCORE2	14726
DDX55_BGHLV17_60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	917					GRCh38	V40	DDX55_BGHLV17_60_CTTGTA_L005_R1_001.fastq.gz,DDX55_BGHLV17_60_CTTGTA_L005_R2_001.fastq.gz		ENCORE2	14575
DDX55_BGHLV17_60_CTTGTA_L005_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	917	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14499
DDX55_BGHLV17_60_CTTGTA_L005_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	917	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14537
DDX55_BGHLV17_60_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	917					GRCh38	V40	DDX55_BGHLV17_60_CTTGTA_L005_R1_001.fastq.gz,DDX55_BGHLV17_60_CTTGTA_L005_R2_001.fastq.gz		ENCORE2	14765
DDX55_BGHLV17_60_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	917					GRCh38	V40	DDX55_BGHLV17_60/Aligned.sortedByCoord.out.bam		ENCORE2	14613
DDX55_BGHLV17_60_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	917					GRCh38	V40	DDX55_BGHLV17_60/Aligned.sortedByCoord.out.bam		ENCORE2	14651
DDX55_BGHLV17_60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	917					GRCh38	V40	DDX55_BGHLV17_60/Aligned.sortedByCoord.out.bam		ENCORE2	14689
DDX55_BGHLV17_60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	917					GRCh38	V40	DDX55_BGHLV17_60/Aligned.sortedByCoord.out.bam		ENCORE2	14727

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