DDX39B RNA-Seq in HepG2

General Information


RBP	DDX39B
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DDX39B-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR224WVD
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR175OSV
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	DDX39B-BGHcLV18-9
Rep2	DDX39B-BGHcLV18-10
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	14.0
Rep2_qPCR	1.0
Rep1_WB	57.2
Rep2_WB	53.4
Antibody Cat#	RN116PW
Antibody Lot#	lot #1
Antibody DCC ID	ENCAB574DNV
Status	Released
Project	ENCODE4
ID	102

Experiment Information (Status: Released)

	BGHcLV18-9	BGHcLV18-10
idx	502	503
TRCN#_or_BGC#	BGC#0000422	BGC#0000422
shRNA_or_gRNA_sequence	CCAGCATGAGTGCATCCCTC	CCAGCATGAGTGCATCCCTC
PAM	AGG	AGG
Name	DDX39B_2	DDX39B_2
Sample_ID	BGHcLV18-9	BGHcLV18-10
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	DDX39B	DDX39B
qPCR_result	14.0	1.0
Ave_qPCR	7.5
RT-qPCR_primer-F	cagtgtttgtcttggccaca
RT-qPCR_primer-R	gcgctcatattccttgctga
protein_conc	3297	3317
WB_result	57.2	53.4
Ave_WB	55.3
WB_DONE_date	8/29/19	WES
MW	49KD
IP	Rabbit / I
antibody_Cat#	RN116PW	lot #1
Antibody DCC ID	ENCAB574DNV
submitted_to_DCC_date
Rep1_TPM	638	0
Rep2_TPM	493	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6655	6656

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DDX39B	Product_ID: RN116PW Lot_ID: 1 Source: MBLI Target Name: DDX39B-human

Experiment Status

	BGHcLV18-9	BGHcLV18-10
Sample_ID	BGHcLV18-9	BGHcLV18-10
Sample Name
Sample Name	DDX39B-BGHcLV18-9	DDX39B-BGHcLV18-10
RBP	DDX39B	DDX39B
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5621	5622

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-9	BGHcLV18-10
Sample #	127	128
Sample Name	DDX39B-BGHcLV18-9	DDX39B-BGHcLV18-10
Sample_Name_Alias
Index Well Position	A05	B05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	3-C2	3-D2
Tecan	26.49	39.31
Tecan_date	2019-12-16	2019-12-16
Size_bp	276	283
Peak_Molarity	27.50	27.40
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/A6.png	DNA_Library_set43-44/set2/B6.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/E7.png	RNA_Library_set43-44/set4/F7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-9	BGHcLV18-10
RBP	DDX39B	DDX39B
Batch_ID	BGHcLV18	BGHcLV18
WB_result	57.200	53.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	703	704

Sequencing Information

	BGHcLV18-9	BGHcLV18-10
Sample_ID	BGHcLV18-9	BGHcLV18-10
Sample Name	DDX39B-BGHcLV18-9	DDX39B-BGHcLV18-10
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	180,295,062	177,609,010
total_aligned_reads	174,903,990	172,859,424
unique_aligned_reads	163,845,220	161,983,238
percent_uniqueAligned	0.90876	0.91202
correlation_replicates	0.998734	0.998734
spikein_reads	384,752	389,708
percent_spikeins	0.00213	0.00219
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	209	210

Data Submission Information

	BGHcLV18-9	BGHcLV18-9	BGHcLV18-9	BGHcLV18-9	BGHcLV18-9	BGHcLV18-9	BGHcLV18-10	BGHcLV18-10	BGHcLV18-10	BGHcLV18-10
ENCODE_alias	brenton-graveley:DDX39B-BGHcLV18	brenton-graveley:DDX39B-BGHcLV18-9	brenton-graveley:L-DDX39B-BGHcLV18-9	brenton-graveley:DDX39B-BGHcLV18-9_S43_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX39B-BGHcLV18-9_S43_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX39B-BGHcLV18-HepG2	brenton-graveley:DDX39B-BGHcLV18-10	brenton-graveley:L-DDX39B-BGHcLV18-10	brenton-graveley:DDX39B-BGHcLV18-10_S44_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DDX39B-BGHcLV18-10_S44_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR175OSV	ENCBS269WJT	ENCLB999KMV	ENCFF742NWQ	ENCFF265GAA	ENCSR224WVD	ENCBS277BUX	ENCLB425VCB	ENCFF065RTJ	ENCFF587WWR
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	BGHcLV18-9	BGHcLV18-9	BGHcLV18-9	BGHcLV18-9	BGHcLV18-9	BGHcLV18-9	BGHcLV18-10	BGHcLV18-10	BGHcLV18-10	BGHcLV18-10
Sample Name	DDX39B-BGHcLV18-9	DDX39B-BGHcLV18-9	DDX39B-BGHcLV18-9	DDX39B-BGHcLV18-9	DDX39B-BGHcLV18-9	DDX39B-BGHcLV18-9	DDX39B-BGHcLV18-10	DDX39B-BGHcLV18-10	DDX39B-BGHcLV18-10	DDX39B-BGHcLV18-10
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		DDX39B-BGHcLV18-9.pdf	L-DDX39B-BGHcLV18-10.pdf				DDX39B-BGHcLV18-10.pdf	L-DDX39B-BGHcLV18-9.pdf
ID	49	178	344	594	646	7178	179	345	595	647

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
DDX39B-BGHcLV18-9_S43_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	209	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	176
DDX39B-BGHcLV18-9_S43_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	209	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	228
DDX39B-BGHcLV18-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	209					GRCh38	V40	DDX39B-BGHcLV18-9_S43_R1_001.filtered.trimmed.paired.fastq.gz,DDX39B-BGHcLV18-9_S43_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24896
DDX39B-BGHcLV18-9_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	209					GRCh38	V40	DDX39B-BGHcLV18-9/Aligned.sortedByCoord.out.bam		ENCORE2	24948
DDX39B-BGHcLV18-9_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	209					GRCh38	V40	DDX39B-BGHcLV18-9/Aligned.sortedByCoord.out.bam		ENCORE2	25000
DDX39B-BGHcLV18-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	209					GRCh38	V40	DDX39B-BGHcLV18-9/Aligned.sortedByCoord.out.bam		ENCORE2	25052
DDX39B-BGHcLV18-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	209					GRCh38	V40	DDX39B-BGHcLV18-9/Aligned.sortedByCoord.out.bam		ENCORE2	25104
DDX39B-BGHcLV18-9_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	209					GRCh38	V40	DDX39B-BGHcLV18-9_S43_R1_001.filtered.trimmed.paired.fastq.gz,DDX39B-BGHcLV18-9_S43_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25156
DDX39B-BGHcLV18-10_S44_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	210	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	175
DDX39B-BGHcLV18-10_S44_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	210	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	227
DDX39B-BGHcLV18-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	210					GRCh38	V40	DDX39B-BGHcLV18-10_S44_R1_001.filtered.trimmed.paired.fastq.gz,DDX39B-BGHcLV18-10_S44_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24895
DDX39B-BGHcLV18-10_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	210					GRCh38	V40	DDX39B-BGHcLV18-10/Aligned.sortedByCoord.out.bam		ENCORE2	24947
DDX39B-BGHcLV18-10_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	210					GRCh38	V40	DDX39B-BGHcLV18-10/Aligned.sortedByCoord.out.bam		ENCORE2	24999
DDX39B-BGHcLV18-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	210					GRCh38	V40	DDX39B-BGHcLV18-10/Aligned.sortedByCoord.out.bam		ENCORE2	25051
DDX39B-BGHcLV18-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	210					GRCh38	V40	DDX39B-BGHcLV18-10/Aligned.sortedByCoord.out.bam		ENCORE2	25103
DDX39B-BGHcLV18-10_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	210					GRCh38	V40	DDX39B-BGHcLV18-10_S44_R1_001.filtered.trimmed.paired.fastq.gz,DDX39B-BGHcLV18-10_S44_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25155