DDX28 RNA-Seq in HepG2

General Information


RBP	DDX28
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX28-BGHLV17-HepG2
ENCODE_series_ID	ENCSR040HJW
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR222CSF
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	DDX28_BGHLV17_55
Rep2	DDX28_BGHLV17_56
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	88.3
Rep2_qPCR	75.0
Rep1_WB
Rep2_WB
Antibody Cat#	A300-761A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB993HVI
Status	Released
Project	ENCODE3
ID	431

Experiment Information (Status: Released)

	BGHLV17-55	BGHLV17-56
idx	291	292
TRCN#_or_BGC#	TRCN0000051762	TRCN0000051762
shRNA_or_gRNA_sequence	CCTGGTTCAGAAGATTGAGCT	CCTGGTTCAGAAGATTGAGCT
PAM
Name	DDX28	DDX28
Sample_ID	BGHLV17-55	BGHLV17-56
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	DDX28	DDX28
qPCR_result	88.3	75.0
Ave_qPCR	81.7
RT-qPCR_primer-F	gcaccgtcatcagttttgtg
RT-qPCR_primer-R	aaggctctttcaccgaggat
protein_conc	3270	3147
WB_result
Ave_WB	no band	no band
WB_DONE_date	1/8/2015
MW
IP	1	1
antibody_Cat#	A300-761A	A300-761A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	2.9	0
Rep2_TPM	2.5	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2356	2357

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV17-55	BGHLV17-56
Sample_ID	BGHLV17-55	BGHLV17-56
Sample Name	DDX28_BGHLV17_55	DDX28_BGHLV17_56
Sample Name	DDX28_BGHLV17_55	DDX28_BGHLV17_56
RBP	DDX28	DDX28
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	588	589

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-55	BGHLV17-56
Sample #
Sample Name	DDX28-BGHLV17-55	DDX28-BGHLV17-56
Sample_Name_Alias	DDX28_BGHLV17_55	DDX28_BGHLV17_56
Index Well Position	S09	S10
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/A5.png	DNA_Library_LV16-17/set1/B5.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/A7.png	RNA_Library_LV16-17-18/set1/B7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-55	BGHLV17-56
RBP	DDX28	DDX28
Batch_ID	BGHLV17	BGHLV17
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2272	2273

Sequencing Information

	BGHLV17-55	BGHLV17-56
Sample_ID	BGHLV17-55	BGHLV17-56
Sample Name	DDX28_BGHLV17_55	DDX28_BGHLV17_56
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	28,830,000	56,780,000
total_aligned_reads	25,097,540	51,003,530
unique_aligned_reads	23,733,542	48,123,570
percent_uniqueAligned	0.82322	0.84754
correlation_replicates	0.978020	0.978020
spikein_reads	64,252	74,764
percent_spikeins	0.00223	0.00132
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	914	915

Data Submission Information

	BGHLV17-55	BGHLV17-55
ENCODE_alias	brenton-graveley:DDX28_BGHLV17	brenton-graveley:DDX28-BGHLV17-HepG2
ENCODE_accession	ENCSR222CSF	ENCSR040HJW
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-55	BGHLV17-55
Sample Name	DDX28_BGHLV17_55	DDX28_BGHLV17_55
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2862	6649

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
DDX28_BGHLV17_55_GATCAG_L005_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	914	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	14496
DDX28_BGHLV17_55_GATCAG_L005_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	914	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	14534
DDX28_BGHLV17_55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	914					GRCh38	V40	DDX28_BGHLV17_55_GATCAG_L005_R1_001.fastq.gz,DDX28_BGHLV17_55_GATCAG_L005_R2_001.fastq.gz		ENCORE2	14572
DDX28_BGHLV17_55_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	914					GRCh38	V40	DDX28_BGHLV17_55/Aligned.sortedByCoord.out.bam		ENCORE2	14610
DDX28_BGHLV17_55_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	914					GRCh38	V40	DDX28_BGHLV17_55/Aligned.sortedByCoord.out.bam		ENCORE2	14648
DDX28_BGHLV17_55_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	914					GRCh38	V40	DDX28_BGHLV17_55/Aligned.sortedByCoord.out.bam		ENCORE2	14686
DDX28_BGHLV17_55_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	914					GRCh38	V40	DDX28_BGHLV17_55/Aligned.sortedByCoord.out.bam		ENCORE2	14724
DDX28_BGHLV17_55_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	914					GRCh38	V40	DDX28_BGHLV17_55_GATCAG_L005_R1_001.fastq.gz,DDX28_BGHLV17_55_GATCAG_L005_R2_001.fastq.gz		ENCORE2	14762
DDX28_BGHLV17_56_TAGCTT_L005_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	915	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	14497
DDX28_BGHLV17_56_TAGCTT_L005_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	915	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	14535
DDX28_BGHLV17_56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	915					GRCh38	V40	DDX28_BGHLV17_56_TAGCTT_L005_R1_001.fastq.gz,DDX28_BGHLV17_56_TAGCTT_L005_R2_001.fastq.gz		ENCORE2	14573
DDX28_BGHLV17_56_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	915					GRCh38	V40	DDX28_BGHLV17_56/Aligned.sortedByCoord.out.bam		ENCORE2	14611
DDX28_BGHLV17_56_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	915					GRCh38	V40	DDX28_BGHLV17_56/Aligned.sortedByCoord.out.bam		ENCORE2	14649
DDX28_BGHLV17_56_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	915					GRCh38	V40	DDX28_BGHLV17_56/Aligned.sortedByCoord.out.bam		ENCORE2	14687
DDX28_BGHLV17_56_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	915					GRCh38	V40	DDX28_BGHLV17_56/Aligned.sortedByCoord.out.bam		ENCORE2	14725
DDX28_BGHLV17_56_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	915					GRCh38	V40	DDX28_BGHLV17_56_TAGCTT_L005_R1_001.fastq.gz,DDX28_BGHLV17_56_TAGCTT_L005_R2_001.fastq.gz		ENCORE2	14763