DUS3L RNA-Seq in HepG2

General Information


RBP	DUS3L
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DUS3L-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR546LZT
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR020EBN
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	DUS3L-BGHcLV18-13
Rep2	DUS3L-BGHcLV18-14
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	32.3
Rep2_qPCR	44.4
Rep1_WB	77.9
Rep2_WB	75.5
Antibody Cat#	PA5-59757
Antibody Lot#	lot# UC2739268A
Antibody DCC ID	ENCAB967CUW
Status	Released
Project	ENCODE4
ID	104

Experiment Information (Status: Released)

	BGHcLV18-13	BGHcLV18-14
idx	506	507
TRCN#_or_BGC#	BGC#0000443	BGC#0000443
shRNA_or_gRNA_sequence	CGAAGCGCTTGCAGATCCGT	CGAAGCGCTTGCAGATCCGT
PAM	CGG	CGG
Name	DUS3L_99	DUS3L_99
Sample_ID	BGHcLV18-13	BGHcLV18-14
transduction_Date	8/13/19	8/13/19
days	D6	D6
RBP_name	DUS3L	DUS3L
qPCR_result	32.3	44.4
Ave_qPCR	38.4
RT-qPCR_primer-F	ACTAGCACCCCTCCCAGC
RT-qPCR_primer-R	GGTAAAGTTTGCCACGGATG
protein_conc	3468	3933
WB_result	77.9	75.5
Ave_WB	76.7
WB_DONE_date	8/22/19	wes
MW	73KD
IP	Rabbit / I
antibody_Cat#	PA5-59757	lot# UC2739268A
Antibody DCC ID	ENCAB967CUW
submitted_to_DCC_date
Rep1_TPM	30	0
Rep2_TPM	11	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6659	6660

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DUS3L	Product_ID: PA5-59757 Lot_ID: UC2739268A Source: Thermo Fisher Target Name: DUS3L-human

Experiment Status

	BGHcLV18-13	BGHcLV18-14
Sample_ID	BGHcLV18-13	BGHcLV18-14
Sample Name
Sample Name	DUS3L-BGHcLV18-13	DUS3L-BGHcLV18-14
RBP	DUS3L	DUS3L
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5625	5626

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-13	BGHcLV18-14
Sample #	131	132
Sample Name	DUS3L-BGHcLV18-13	DUS3L-BGHcLV18-14
Sample_Name_Alias
Index Well Position	E05	F05
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-G2	3-H2
Tecan	39.84	35.74
Tecan_date	2019-12-16	2019-12-16
Size_bp	295	276
Peak_Molarity	22.50	29.20
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/E6.png	DNA_Library_set43-44/set2/F6.png
RIN	9.5	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/A8.png	RNA_Library_set43-44/set4/B8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-13	BGHcLV18-14
RBP	DUS3L	DUS3L
Batch_ID	BGHcLV18	BGHcLV18
WB_result	77.900	75.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	707	708

Sequencing Information

	BGHcLV18-13	BGHcLV18-14
Sample_ID	BGHcLV18-13	BGHcLV18-14
Sample Name	DUS3L-BGHcLV18-13	DUS3L-BGHcLV18-14
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	195,782,768	187,406,808
total_aligned_reads	188,388,254	178,482,954
unique_aligned_reads	176,199,768	166,787,044
percent_uniqueAligned	0.89998	0.88997
correlation_replicates	0.996189	0.996189
spikein_reads	298,104	305,460
percent_spikeins	0.00152	0.00163
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	213	214

Data Submission Information

	BGHcLV18-13	BGHcLV18-13	BGHcLV18-13	BGHcLV18-13	BGHcLV18-13	BGHcLV18-13	BGHcLV18-14	BGHcLV18-14	BGHcLV18-14	BGHcLV18-14
ENCODE_alias	brenton-graveley:DUS3L-BGHcLV18	brenton-graveley:DUS3L-BGHcLV18-13	brenton-graveley:L-DUS3L-BGHcLV18-13	brenton-graveley:DUS3L-BGHcLV18-13_S47_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DUS3L-BGHcLV18-13_S47_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DUS3L-BGHcLV18-HepG2	brenton-graveley:DUS3L-BGHcLV18-14	brenton-graveley:L-DUS3L-BGHcLV18-14	brenton-graveley:DUS3L-BGHcLV18-14_S48_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DUS3L-BGHcLV18-14_S48_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR020EBN	ENCBS699NLD	ENCLB850GUR	ENCFF603HYQ	ENCFF726DVL	ENCSR546LZT	ENCBS902VWJ	ENCLB027CND	ENCFF990GBY	ENCFF260HRX
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	BGHcLV18-13	BGHcLV18-13	BGHcLV18-13	BGHcLV18-13	BGHcLV18-13	BGHcLV18-13	BGHcLV18-14	BGHcLV18-14	BGHcLV18-14	BGHcLV18-14
Sample Name	DUS3L-BGHcLV18-13	DUS3L-BGHcLV18-13	DUS3L-BGHcLV18-13	DUS3L-BGHcLV18-13	DUS3L-BGHcLV18-13	DUS3L-BGHcLV18-13	DUS3L-BGHcLV18-14	DUS3L-BGHcLV18-14	DUS3L-BGHcLV18-14	DUS3L-BGHcLV18-14
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		DUS3L-BGHcLV18-13.pdf	L-DUS3L-BGHcLV18-13.pdf				DUS3L-BGHcLV18-14.pdf	L-DUS3L-BGHcLV18-14.pdf
ID	51	182	348	598	650	7192	183	349	599	651

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
DUS3L-BGHcLV18-13_S47_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	213	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	179
DUS3L-BGHcLV18-13_S47_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	213	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	231
DUS3L-BGHcLV18-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	213					GRCh38	V40	DUS3L-BGHcLV18-13_S47_R1_001.filtered.trimmed.paired.fastq.gz,DUS3L-BGHcLV18-13_S47_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24899
DUS3L-BGHcLV18-13_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	213					GRCh38	V40	DUS3L-BGHcLV18-13/Aligned.sortedByCoord.out.bam		ENCORE2	24951
DUS3L-BGHcLV18-13_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	213					GRCh38	V40	DUS3L-BGHcLV18-13/Aligned.sortedByCoord.out.bam		ENCORE2	25003
DUS3L-BGHcLV18-13_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	213					GRCh38	V40	DUS3L-BGHcLV18-13/Aligned.sortedByCoord.out.bam		ENCORE2	25055
DUS3L-BGHcLV18-13_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	213					GRCh38	V40	DUS3L-BGHcLV18-13/Aligned.sortedByCoord.out.bam		ENCORE2	25107
DUS3L-BGHcLV18-13_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	213					GRCh38	V40	DUS3L-BGHcLV18-13_S47_R1_001.filtered.trimmed.paired.fastq.gz,DUS3L-BGHcLV18-13_S47_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25159
DUS3L-BGHcLV18-14_S48_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	214	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	180
DUS3L-BGHcLV18-14_S48_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	214	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	232
DUS3L-BGHcLV18-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	214					GRCh38	V40	DUS3L-BGHcLV18-14_S48_R1_001.filtered.trimmed.paired.fastq.gz,DUS3L-BGHcLV18-14_S48_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24900
DUS3L-BGHcLV18-14_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	214					GRCh38	V40	DUS3L-BGHcLV18-14/Aligned.sortedByCoord.out.bam		ENCORE2	24952
DUS3L-BGHcLV18-14_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	214					GRCh38	V40	DUS3L-BGHcLV18-14/Aligned.sortedByCoord.out.bam		ENCORE2	25004
DUS3L-BGHcLV18-14_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	214					GRCh38	V40	DUS3L-BGHcLV18-14/Aligned.sortedByCoord.out.bam		ENCORE2	25056
DUS3L-BGHcLV18-14_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	214					GRCh38	V40	DUS3L-BGHcLV18-14/Aligned.sortedByCoord.out.bam		ENCORE2	25108
DUS3L-BGHcLV18-14_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	214					GRCh38	V40	DUS3L-BGHcLV18-14_S48_R1_001.filtered.trimmed.paired.fastq.gz,DUS3L-BGHcLV18-14_S48_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25160