DUS3L RNA-Seq in K562

General Information


RBP	DUS3L
Cell_Line	K562
Method	CRISPR
Exp_Name	DUS3L-BGKcLV17-K562
ENCODE_series_ID	ENCSR327GCA
Batch_ID	BGKcLV17
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR949QWR
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	DUS3L-BGKcLV17-13
Rep2	DUS3L-BGKcLV17-14
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR	66.6
Rep2_qPCR	62.3
Rep1_WB	68.1
Rep2_WB	70.4
Antibody Cat#	PA5-59757
Antibody Lot#	lot# UC2739268A
Antibody DCC ID	ENCAB967CUW
Status	Released
Project	ENCODE4
ID	145

Experiment Information (Status: Released)

	BGKcLV17-13	BGKcLV17-14
idx	620	621
TRCN#_or_BGC#	BGC#0000443	BGC#0000443
shRNA_or_gRNA_sequence	CGAAGCGCTTGCAGATCCGT	CGAAGCGCTTGCAGATCCGT
PAM	CGG	CGG
Name	DUS3L_99	DUS3L_99
Sample_ID	BGKcLV17-13	BGKcLV17-14
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	DUS3L	DUS3L
qPCR_result	66.6	62.3
Ave_qPCR	64.5
RT-qPCR_primer-F	ACTAGCACCCCTCCCAGC
RT-qPCR_primer-R	GGTAAAGTTTGCCACGGATG
protein_conc	4665	4450
WB_result	68.1	70.4
Ave_WB	69.2
WB_DONE_date	7/10/19	WES
MW	73KD
IP	Rabbit / I
antibody_Cat#	PA5-59757	lot# UC2739268A
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	59.48	0
Rep2_TPM	56.87	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4736	4737

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

	BGKcLV17-13	BGKcLV17-14
Sample_ID	BGKcLV17-13	BGKcLV17-14
Sample Name
Sample Name	DUS3L-BGKcLV17-13	DUS3L-BGKcLV17-14
RBP	DUS3L	DUS3L
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5497	5498

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-13	BGKcLV17-14
Sample #	87	88
Sample Name	DUS3L-BGKcLV17-13	DUS3L-BGKcLV17-14
Sample_Name_Alias
Index Well Position	C11	D11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	1-E2	1-F2
Tecan	30.15	24.49
Tecan_date	2019-12-10	2019-12-10
Size_bp	277	277
Peak_Molarity	22.70	23.60
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/E7.png	DNA_Library_set43-44/set1/F7.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_set43-44/set4/E2.png	RNA_Library_set43-44/set4/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-13	BGKcLV17-14
RBP	DUS3L	DUS3L
Batch_ID	BGKcLV17	BGKcLV17
WB_result	68.100	70.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	663	664

Sequencing Information

	BGKcLV17-13	BGKcLV17-14
Sample_ID	BGKcLV17-13	BGKcLV17-14
Sample Name	DUS3L-BGKcLV17-13	DUS3L-BGKcLV17-14
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	105,377,902	270,679,642
total_aligned_reads	97,566,126	241,648,182
unique_aligned_reads	89,046,478	219,553,486
percent_uniqueAligned	0.84502	0.81112
correlation_replicates	0.999534	0.999534
spikein_reads	31,734	89,610
percent_spikeins	0.00030	0.00033
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	165	166

Data Submission Information

	BGKcLV17-13	BGKcLV17-13	BGKcLV17-13	BGKcLV17-13	BGKcLV17-13	BGKcLV17-13	BGKcLV17-14	BGKcLV17-14	BGKcLV17-14	BGKcLV17-14
ENCODE_alias	brenton-graveley:DUS3L-BGKcLV17	brenton-graveley:DUS3L-BGKcLV17-13	brenton-graveley:L-DUS3L-BGKcLV17-13	brenton-graveley:DUS3L-BGKcLV17-13_S83_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DUS3L-BGKcLV17-13_S83_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DUS3L-BGKcLV17-K562	brenton-graveley:DUS3L-BGKcLV17-14	brenton-graveley:L-DUS3L-BGKcLV17-14	brenton-graveley:DUS3L-BGKcLV17-14_S84_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DUS3L-BGKcLV17-14_S84_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR949QWR	ENCBS692AVF	ENCLB607ZFY	ENCFF933ZOW	ENCFF405HHD	ENCSR327GCA	ENCBS989ODK	ENCLB718JGF	ENCFF023HON	ENCFF677WPO
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	BGKcLV17-13	BGKcLV17-13	BGKcLV17-13	BGKcLV17-13	BGKcLV17-13	BGKcLV17-13	BGKcLV17-14	BGKcLV17-14	BGKcLV17-14	BGKcLV17-14
Sample Name	DUS3L-BGKcLV17-13	DUS3L-BGKcLV17-13	DUS3L-BGKcLV17-13	DUS3L-BGKcLV17-13	DUS3L-BGKcLV17-13	DUS3L-BGKcLV17-13	DUS3L-BGKcLV17-14	DUS3L-BGKcLV17-14	DUS3L-BGKcLV17-14	DUS3L-BGKcLV17-14
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	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
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		DUS3L-BGKcLV17-13.pdf	L-DUS3L-BGKcLV17-13.pdf				DUS3L-BGKcLV17-14.pdf	L-DUS3L-BGKcLV17-14.pdf
ID	42	166	330	528	580	7193	167	331	529	581

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-BGKcLV17-13_S83_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	165	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	79
DUS3L-BGKcLV17-13_S83_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	165	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	131
DUS3L-BGKcLV17-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	165					GRCh38	V40	DUS3L-BGKcLV17-13_S83_R1_001.filtered.trimmed.paired.fastq.gz,DUS3L-BGKcLV17-13_S83_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24370
DUS3L-BGKcLV17-13_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	165					GRCh38	V40	DUS3L-BGKcLV17-13/Aligned.sortedByCoord.out.bam		ENCORE2	24422
DUS3L-BGKcLV17-13_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	165					GRCh38	V40	DUS3L-BGKcLV17-13/Aligned.sortedByCoord.out.bam		ENCORE2	24474
DUS3L-BGKcLV17-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	165					GRCh38	V40	DUS3L-BGKcLV17-13/Aligned.sortedByCoord.out.bam		ENCORE2	24526
DUS3L-BGKcLV17-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	165					GRCh38	V40	DUS3L-BGKcLV17-13/Aligned.sortedByCoord.out.bam		ENCORE2	24578
DUS3L-BGKcLV17-13_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	165					GRCh38	V40	DUS3L-BGKcLV17-13_S83_R1_001.filtered.trimmed.paired.fastq.gz,DUS3L-BGKcLV17-13_S83_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24630
DUS3L-BGKcLV17-14_S84_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	166	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	80
DUS3L-BGKcLV17-14_S84_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	166	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	132
DUS3L-BGKcLV17-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	166					GRCh38	V40	DUS3L-BGKcLV17-14_S84_R1_001.filtered.trimmed.paired.fastq.gz,DUS3L-BGKcLV17-14_S84_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24371
DUS3L-BGKcLV17-14_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	166					GRCh38	V40	DUS3L-BGKcLV17-14/Aligned.sortedByCoord.out.bam		ENCORE2	24423
DUS3L-BGKcLV17-14_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	166					GRCh38	V40	DUS3L-BGKcLV17-14/Aligned.sortedByCoord.out.bam		ENCORE2	24475
DUS3L-BGKcLV17-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	166					GRCh38	V40	DUS3L-BGKcLV17-14/Aligned.sortedByCoord.out.bam		ENCORE2	24527
DUS3L-BGKcLV17-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	166					GRCh38	V40	DUS3L-BGKcLV17-14/Aligned.sortedByCoord.out.bam		ENCORE2	24579
DUS3L-BGKcLV17-14_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	166					GRCh38	V40	DUS3L-BGKcLV17-14_S84_R1_001.filtered.trimmed.paired.fastq.gz,DUS3L-BGKcLV17-14_S84_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24631