DDX24 RNA-Seq in HepG2

General Information


RBP	DDX24
Cell_Line	HepG2
Method	shRNA
Exp_Name	DDX24-BGHLV14-HepG2
ENCODE_series_ID	ENCSR691YZD
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR300IEW
ENCODE_CN_Exp_ID	ENCSR003EKR
Rep1	DDX24_BGHLV14-11
Rep2	DDX24_BGHLV14-12
CN1	NT_BGHLV14-1_1
CN2	NT_BGHLV14-2_1
Rep1_qPCR	71.1
Rep2_qPCR	76.5
Rep1_WB	88.5
Rep2_WB	87.7
Antibody Cat#	A300-696A
Antibody Lot#	A300-696A
Antibody DCC ID	ENCAB988AYG
Status	Released
Project	ENCODE3
ID	388

Experiment Information (Status: Released)

	BGHLV14-11	BGHLV14-12
idx	105	106
TRCN#_or_BGC#	TRCN0000050314	TRCN0000050314
shRNA_or_gRNA_sequence	CGCTCAAGAAAGATGAGGATA	CGCTCAAGAAAGATGAGGATA
PAM
Name	DDX24	DDX24
Sample_ID	BGHLV14-11	BGHLV14-12
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	DDX24	DDX24
qPCR_result	71.1	76.5
Ave_qPCR	73.8
RT-qPCR_primer-F	AACTCTTGGATTGAGCAGGC
RT-qPCR_primer-R	GTCTCCGACGTTCTTCTTGC
protein_conc	4153	3955
WB_result	88.5	87.7
Ave_WB	88.1
WB_DONE_date	7/27/2015
MW	96kDa
IP	1	1
antibody_Cat#	A300-696A	A300-696A
Antibody DCC ID	ENCAB988AYG	ENCAB988AYG
submitted_to_DCC_date	8/6/2015
Rep1_TPM	38.4	0
Rep2_TPM	42.3	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	2162	2163

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX24	Product_ID: A300-696A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX24-human

Experiment Status

	BGHLV14-11	BGHLV14-12
Sample_ID	BGHLV14-11	BGHLV14-12
Sample Name	DDX24_BGHLV14-11	DDX24_BGHLV14-12
Sample Name	DDX24_BGHLV14-11	DDX24_BGHLV14-12
RBP	DDX24	DDX24
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	498	499

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-11	BGHLV14-12
Sample #
Sample Name	DDX24-BGHLV14-11	DDX24-BGHLV14-12
Sample_Name_Alias	DDX24_BGHLV14-11	DDX24_BGHLV14-12
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/H8.png	DNA_Library_LV13-14/set1/A9.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/C5.png	RNA_Library_LV13-14-16/set1/D5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-11	BGHLV14-12
RBP	DDX24	DDX24
Batch_ID	BGHLV14	BGHLV14
WB_result	88.500	87.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2182	2183

Sequencing Information

	BGHLV14-11	BGHLV14-12
Sample_ID	BGHLV14-11	BGHLV14-12
Sample Name	DDX24_BGHLV14-11	DDX24_BGHLV14-12
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	58,110,000	53,730,000
total_aligned_reads	54,858,566	50,618,860
unique_aligned_reads	51,580,840	47,654,182
percent_uniqueAligned	0.88764	0.88692
correlation_replicates	0.996096	0.996096
spikein_reads	183,382	134,718
percent_spikeins	0.00316	0.00251
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	824	825

Data Submission Information

	BGHLV14-11	BGHLV14-11
ENCODE_alias	brenton-graveley:DDX24_BGHLV14	brenton-graveley:DDX24-BGHLV14-HepG2
ENCODE_accession	ENCSR300IEW	ENCSR691YZD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-11	BGHLV14-11
Sample Name	DDX24_BGHLV14-11	DDX24_BGHLV14-11
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2799	6645

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
DDX24_BGHLV14-11_ATGTCA_L001_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	824	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13790
DDX24_BGHLV14-11_ATGTCA_L001_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	824	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13852
DDX24_BGHLV14-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	824					GRCh38	V40	DDX24_BGHLV14-11_ATGTCA_L001_R1_001.fastq.gz,DDX24_BGHLV14-11_ATGTCA_L001_R2_001.fastq.gz		ENCORE2	13914
DDX24_BGHLV14-11_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	824					GRCh38	V40	DDX24_BGHLV14-11/Aligned.sortedByCoord.out.bam		ENCORE2	13976
DDX24_BGHLV14-11_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	824					GRCh38	V40	DDX24_BGHLV14-11/Aligned.sortedByCoord.out.bam		ENCORE2	14038
DDX24_BGHLV14-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	824					GRCh38	V40	DDX24_BGHLV14-11/Aligned.sortedByCoord.out.bam		ENCORE2	14100
DDX24_BGHLV14-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	824					GRCh38	V40	DDX24_BGHLV14-11/Aligned.sortedByCoord.out.bam		ENCORE2	14162
DDX24_BGHLV14-11_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	824					GRCh38	V40	DDX24_BGHLV14-11_ATGTCA_L001_R1_001.fastq.gz,DDX24_BGHLV14-11_ATGTCA_L001_R2_001.fastq.gz		ENCORE2	14224
DDX24_BGHLV14-12_CCGTCC_L001_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	825	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13791
DDX24_BGHLV14-12_CCGTCC_L001_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	825	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13853
DDX24_BGHLV14-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	825					GRCh38	V40	DDX24_BGHLV14-12_CCGTCC_L001_R1_001.fastq.gz,DDX24_BGHLV14-12_CCGTCC_L001_R2_001.fastq.gz		ENCORE2	13915
DDX24_BGHLV14-12_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	825					GRCh38	V40	DDX24_BGHLV14-12/Aligned.sortedByCoord.out.bam		ENCORE2	13977
DDX24_BGHLV14-12_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	825					GRCh38	V40	DDX24_BGHLV14-12/Aligned.sortedByCoord.out.bam		ENCORE2	14039
DDX24_BGHLV14-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	825					GRCh38	V40	DDX24_BGHLV14-12/Aligned.sortedByCoord.out.bam		ENCORE2	14101
DDX24_BGHLV14-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	825					GRCh38	V40	DDX24_BGHLV14-12/Aligned.sortedByCoord.out.bam		ENCORE2	14163
DDX24_BGHLV14-12_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	825					GRCh38	V40	DDX24_BGHLV14-12_CCGTCC_L001_R1_001.fastq.gz,DDX24_BGHLV14-12_CCGTCC_L001_R2_001.fastq.gz		ENCORE2	14225