DDX27 RNA-Seq in HepG2

General Information


RBP	DDX27
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX27-BGHLV17-HepG2
ENCODE_series_ID	ENCSR377KWX
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR210RWL
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	DDX27_BGHLV17_53
Rep2	DDX27_BGHLV17_54
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	76.5
Rep2_qPCR	76.2
Rep1_WB	98.1
Rep2_WB	94.5
Antibody Cat#	A302-217A
Antibody Lot#	A302-217A
Antibody DCC ID	ENCAB626TGL
Status	Released
Project	ENCODE3
ID	430

Experiment Information (Status: Released)

	BGHLV17-53	BGHLV17-54
idx	289	290
TRCN#_or_BGC#	TRCN0000050003	TRCN0000050003
shRNA_or_gRNA_sequence	GCAGAGGAAAGGTCTCAGTTT	GCAGAGGAAAGGTCTCAGTTT
PAM
Name	DDX27	DDX27
Sample_ID	BGHLV17-53	BGHLV17-54
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	DDX27	DDX27
qPCR_result	76.5	76.2
Ave_qPCR	76.3
RT-qPCR_primer-F	agaaggggaaggaggcagt
RT-qPCR_primer-R	gcagagctttggcaattttc
protein_conc	2948	2981
WB_result	98.1	94.5
Ave_WB	96.3
WB_DONE_date	4/7/2015
MW
IP	1	1
antibody_Cat#	A302-217A	A302-217A
Antibody DCC ID	ENCAB626TGL	ENCAB626TGL
submitted_to_DCC_date	5/4/2015
Rep1_TPM	43.1	0
Rep2_TPM	46.6	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2354	2355

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX27	Product_ID: A302-217A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX27-human

Experiment Status

	BGHLV17-53	BGHLV17-54
Sample_ID	BGHLV17-53	BGHLV17-54
Sample Name	DDX27_BGHLV17_53	DDX27_BGHLV17_54
Sample Name	DDX27_BGHLV17_53	DDX27_BGHLV17_54
RBP	DDX27	DDX27
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	586	587

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-53	BGHLV17-54
Sample #
Sample Name	DDX27-BGHLV17-53	DDX27-BGHLV17-54
Sample_Name_Alias	DDX27_BGHLV17_53	DDX27_BGHLV17_54
Index Well Position	S07	S08
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/G4.png	DNA_Library_LV16-17/set1/H4.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/G6.png	RNA_Library_LV16-17-18/set1/H6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-53	BGHLV17-54
RBP	DDX27	DDX27
Batch_ID	BGHLV17	BGHLV17
WB_result	98.100	94.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2270	2271

Sequencing Information

	BGHLV17-53	BGHLV17-54	BGHLV17-54
Sample_ID	BGHLV17-53	BGHLV17-54	BGHLV17-54
Sample Name	DDX27_BGHLV17_53	DDX27_BGHLV17_54	DDX27_BGHLV17_54
Pool ID	Pool-141001	Pool-141001	Pool-151215B
LocalServer_folder	set17	set17	set17
total_reads	36,880,000	16,050,000	80,541,398
total_aligned_reads	33,908,180	14,768,632	68,074,574
unique_aligned_reads	32,070,652	13,980,500	64,345,560
percent_uniqueAligned	0.86959	0.87106	0.79891
correlation_replicates	0.996102	0.996102
spikein_reads	70,926	36,048	171,924
percent_spikeins	0.00192	0.00225	0.00213
original_ReadLength	100	100	100
QC_Status	Submitted	Submitted	Submitted
ID	912	913	1376

Data Submission Information

	BGHLV17-53	BGHLV17-53
ENCODE_alias	brenton-graveley:DDX27_BGHLV17	brenton-graveley:DDX27-BGHLV17-HepG2
ENCODE_accession	ENCSR210RWL	ENCSR377KWX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-53	BGHLV17-53
Sample Name	DDX27_BGHLV17_53	DDX27_BGHLV17_53
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2861	6647

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
DDX27_BGHLV17_53_CAGATC_L004_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	912	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	14494
DDX27_BGHLV17_53_CAGATC_L004_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	912	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	14532
DDX27_BGHLV17_53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	912					GRCh38	V40	DDX27_BGHLV17_53_CAGATC_L004_R1_001.fastq.gz,DDX27_BGHLV17_53_CAGATC_L004_R2_001.fastq.gz		ENCORE2	14570
DDX27_BGHLV17_53_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	912					GRCh38	V40	DDX27_BGHLV17_53/Aligned.sortedByCoord.out.bam		ENCORE2	14608
DDX27_BGHLV17_53_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	912					GRCh38	V40	DDX27_BGHLV17_53/Aligned.sortedByCoord.out.bam		ENCORE2	14646
DDX27_BGHLV17_53_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	912					GRCh38	V40	DDX27_BGHLV17_53/Aligned.sortedByCoord.out.bam		ENCORE2	14684
DDX27_BGHLV17_53_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	912					GRCh38	V40	DDX27_BGHLV17_53/Aligned.sortedByCoord.out.bam		ENCORE2	14722
DDX27_BGHLV17_53_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	912					GRCh38	V40	DDX27_BGHLV17_53_CAGATC_L004_R1_001.fastq.gz,DDX27_BGHLV17_53_CAGATC_L004_R2_001.fastq.gz		ENCORE2	14760
DDX27_BGHLV17_54_ACTTGA_L004_R1_001.merged.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	913	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	14495
DDX27_BGHLV17_54_ACTTGA_L004_R2_001.merged.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	913	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	14533
DDX27_BGHLV17_54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	913					GRCh38	V40	DDX27_BGHLV17_54_ACTTGA_L004_R1_001.merged.fastq.gz,DDX27_BGHLV17_54_ACTTGA_L004_R2_001.merged.fastq.gz		ENCORE2	14571
DDX27_BGHLV17_54_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	913					GRCh38	V40	DDX27_BGHLV17_54/Aligned.sortedByCoord.out.bam		ENCORE2	14609
DDX27_BGHLV17_54_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	913					GRCh38	V40	DDX27_BGHLV17_54/Aligned.sortedByCoord.out.bam		ENCORE2	14647
DDX27_BGHLV17_54_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	913					GRCh38	V40	DDX27_BGHLV17_54/Aligned.sortedByCoord.out.bam		ENCORE2	14685
DDX27_BGHLV17_54_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	913					GRCh38	V40	DDX27_BGHLV17_54/Aligned.sortedByCoord.out.bam		ENCORE2	14723
DDX27_BGHLV17_54_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	913					GRCh38	V40	DDX27_BGHLV17_54_ACTTGA_L004_R1_001.merged.fastq.gz,DDX27_BGHLV17_54_ACTTGA_L004_R2_001.merged.fastq.gz		ENCORE2	14761