DDX42 RNA-Seq in HepG2

General Information


RBP	DDX42
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DDX42-BGHcLV05-HepG2
ENCODE_series_ID	ENCSR931AJR
Batch_ID	BGHcLV05
Pool ID	Pool-180109
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR718RBZ
ENCODE_CN_Exp_ID	ENCSR834IFU
Rep1	DDX42-BGHcLV05-11C
Rep2	DDX42-BGHcLV05-12C
CN1	NT-BGHcLV05-1C
CN2	NT-BGHcLV05-2C
Rep1_qPCR	8.3
Rep2_qPCR	21.9
Rep1_WB	93.1
Rep2_WB	95.1
Antibody Cat#	A303-353A
Antibody Lot#	A303-353A
Antibody DCC ID	ENCAB455YJZ
Status	Released
Project	ENCODE4
ID	258

Experiment Information (Status: Released)

	BGHcLV05-11	BGHcLV05-11	BGHcLV05-12	BGHcLV05-12
idx	47	84	48	85
TRCN#_or_BGC#	BGC#0000030	BGC#0000030	BGC#0000030	BGC#0000030
shRNA_or_gRNA_sequence	GGTGGTCCTGGCACTAAGCG	GGTGGTCCTGGCACTAAGCG	GGTGGTCCTGGCACTAAGCG	GGTGGTCCTGGCACTAAGCG
PAM
Name	DDX42_51	DDX42_51	DDX42_51	DDX42_51
Sample_ID	BGHcLV05-11	BGHcLV05-11	BGHcLV05-12	BGHcLV05-12
transduction_Date	7/12/16	7/12/16	7/12/16	7/12/16
days	DAY 6		DAY 6
RBP_name	DDX42	DDX42	DDX42	DDX42
qPCR_result	8.3		21.9
Ave_qPCR	15.1
RT-qPCR_primer-F	accctattcgagtggtgcag
RT-qPCR_primer-R	cgggtaagccagttccatt
protein_conc	4240	0	3730	0
WB_result	93.1		95.1
Ave_WB	94.1
WB_DONE_date	7/20/16		WES
MW	103 kDa
IP	1
antibody_Cat#	A303-353A		A303-353A
Antibody DCC ID	ENCAB455YJZ		ENCAB455YJZ
submitted_to_DCC_date	10/26/16
Rep1_TPM	106	0	0	0
Rep2_TPM	92	0	0	0
Action	Ready		Ready
Library_start_date	12/18/17		12/18/17
repeat_library
Note
ID	6188	6227	6189	6228

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX42	Product_ID: A303-353A Lot_ID: 1 Source: Bethyl Labs Target Name: DDX42-human

Experiment Status

	BGHcLV05-11	BGHcLV05-12
Sample_ID	BGHcLV05-11	BGHcLV05-12
Sample Name
Sample Name	DDX42-BGHcLV05-11C	DDX42-BGHcLV05-12C
RBP	DDX42	DDX42
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6419	6420

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV05-11	BGHcLV05-12
Sample #	3	4
Sample Name	DDX42-BGHcLV05-11C	DDX42-BGHcLV05-12C
Sample_Name_Alias
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	294	298
Peak_Molarity	18.10	9.66
libSampleQC_DNA_Well	DNA_Library_set40/set1/G7.png	DNA_Library_set40/set1/H7.png
RIN	9.3	9.7
libSample_RNA_Well	RNA_Library_set40/set1/C3.png	RNA_Library_set40/set1/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHcLV05-11	BGHcLV05-12
RBP	DDX42	DDX42
Batch_ID	BGHcLV05	BGHcLV05
WB_result	93.100	95.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	926	927

Sequencing Information

	BGHcLV05-11	BGHcLV05-12
Sample_ID	BGHcLV05-11	BGHcLV05-12
Sample Name	DDX42-BGHcLV05-11C	DDX42-BGHcLV05-12C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_H	set40_H
total_reads	45,261,814	60,424,344
total_aligned_reads	38,540,654	52,140,636
unique_aligned_reads	36,295,882	49,171,606
percent_uniqueAligned	0.80191	0.81377
correlation_replicates	0.996510	0.996510
spikein_reads	6,472	15,170
percent_spikeins	0.00014	0.00025
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	329	330

Data Submission Information

	BGHcLV05-11	BGHcLV05-11	BGHcLV05-11	BGHcLV05-11	BGHcLV05-11	BGHcLV05-11	BGHcLV05-12	BGHcLV05-12	BGHcLV05-12	BGHcLV05-12
ENCODE_alias	brenton-graveley:DDX42-BGHcLV05-C	brenton-graveley:DDX42-BGHcLV05-11C	brenton-graveley:L-DDX42-BGHcLV05-11C	brenton-graveley:DDX42-BGHcLV05-11C_ACTGAT_ACBYWVANXX_L003_001.R1.fastq.gz	brenton-graveley:DDX42-BGHcLV05-11C_ACTGAT_ACBYWVANXX_L003_001.R2.fastq.gz	brenton-graveley:DDX42-BGHcLV05-HepG2	brenton-graveley:DDX42-BGHcLV05-12C	brenton-graveley:L-DDX42-BGHcLV05-12C	brenton-graveley:DDX42-BGHcLV05-12C_ATTCCT_ACBYWVANXX_L003_001.R1.fastq.gz	brenton-graveley:DDX42-BGHcLV05-12C_ATTCCT_ACBYWVANXX_L003_001.R2.fastq.gz
ENCODE_accession	ENCSR718RBZ	ENCBS199IOE	ENCLB961UWW	ENCFF170JPS	ENCFF041BXD	ENCSR931AJR	ENCBS073ZDK	ENCLB676AXT	ENCFF573JFO	ENCFF857IWY
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV05-11	BGHcLV05-11	BGHcLV05-11	BGHcLV05-11	BGHcLV05-11	BGHcLV05-11	BGHcLV05-12	BGHcLV05-12	BGHcLV05-12	BGHcLV05-12
Sample Name	DDX42-BGHcLV05-11C	DDX42-BGHcLV05-11C	DDX42-BGHcLV05-11C	DDX42-BGHcLV05-11C	DDX42-BGHcLV05-11C	DDX42-BGHcLV05-11C	DDX42-BGHcLV05-12C	DDX42-BGHcLV05-12C	DDX42-BGHcLV05-12C	DDX42-BGHcLV05-12C
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol				LV40_biosample_protocol	LV40_library_protocol
protocol_URL		DDX42-BGHcLV05-11C.pdf	L-DDX42-BGHcLV05-11C.pdf				DDX42-BGHcLV05-12C.pdf	L-DDX42-BGHcLV05-12C.pdf
ID	1433	1464	1520	1576	1613	7180	1465	1521	1577	1614

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
DDX42-BGHcLV05-11C_ACTGAT_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	329	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1C_CGTACG_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV05-2C_GAGTGG_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE4	643
DDX42-BGHcLV05-11C_ACTGAT_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	329	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1C_CGTACG_ACBYWVANXX_L003_001.R2.fastq.gz,NT-BGHcLV05-2C_GAGTGG_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE4	685
DDX42-BGHcLV05-11C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	329					GRCh38	V40	DDX42-BGHcLV05-11C_ACTGAT_ACBYWVANXX_L003_001.R1.fastq.gz,DDX42-BGHcLV05-11C_ACTGAT_ACBYWVANXX_L003_001.R2.fastq.gz		ENCORE2	23250
DDX42-BGHcLV05-11C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	329					GRCh38	V40	DDX42-BGHcLV05-11C/Aligned.sortedByCoord.out.bam		ENCORE2	23284
DDX42-BGHcLV05-11C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	329					GRCh38	V40	DDX42-BGHcLV05-11C/Aligned.sortedByCoord.out.bam		ENCORE2	23318
DDX42-BGHcLV05-11C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	329					GRCh38	V40	DDX42-BGHcLV05-11C/Aligned.sortedByCoord.out.bam		ENCORE2	23352
DDX42-BGHcLV05-11C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	329					GRCh38	V40	DDX42-BGHcLV05-11C/Aligned.sortedByCoord.out.bam		ENCORE2	23386
DDX42-BGHcLV05-11C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	329					GRCh38	V40	DDX42-BGHcLV05-11C_ACTGAT_ACBYWVANXX_L003_001.R1.fastq.gz,DDX42-BGHcLV05-11C_ACTGAT_ACBYWVANXX_L003_001.R2.fastq.gz		ENCORE2	23420
DDX42-BGHcLV05-12C_ATTCCT_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	330	HiSeq2500	100	paired-ended	1				NT-BGHcLV05-1C_CGTACG_ACBYWVANXX_L003_001.R1.fastq.gz,NT-BGHcLV05-2C_GAGTGG_ACBYWVANXX_L003_001.R1.fastq.gz	ENCODE4	644
DDX42-BGHcLV05-12C_ATTCCT_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	330	HiSeq2500	100	paired-ended	2				NT-BGHcLV05-1C_CGTACG_ACBYWVANXX_L003_001.R2.fastq.gz,NT-BGHcLV05-2C_GAGTGG_ACBYWVANXX_L003_001.R2.fastq.gz	ENCODE4	686
DDX42-BGHcLV05-12C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	330					GRCh38	V40	DDX42-BGHcLV05-12C_ATTCCT_ACBYWVANXX_L003_001.R1.fastq.gz,DDX42-BGHcLV05-12C_ATTCCT_ACBYWVANXX_L003_001.R2.fastq.gz		ENCORE2	23251
DDX42-BGHcLV05-12C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	330					GRCh38	V40	DDX42-BGHcLV05-12C/Aligned.sortedByCoord.out.bam		ENCORE2	23285
DDX42-BGHcLV05-12C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	330					GRCh38	V40	DDX42-BGHcLV05-12C/Aligned.sortedByCoord.out.bam		ENCORE2	23319
DDX42-BGHcLV05-12C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	330					GRCh38	V40	DDX42-BGHcLV05-12C/Aligned.sortedByCoord.out.bam		ENCORE2	23353
DDX42-BGHcLV05-12C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	330					GRCh38	V40	DDX42-BGHcLV05-12C/Aligned.sortedByCoord.out.bam		ENCORE2	23387
DDX42-BGHcLV05-12C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	330					GRCh38	V40	DDX42-BGHcLV05-12C_ATTCCT_ACBYWVANXX_L003_001.R1.fastq.gz,DDX42-BGHcLV05-12C_ATTCCT_ACBYWVANXX_L003_001.R2.fastq.gz		ENCORE2	23421