DIS3 RNA-Seq in K562

General Information


RBP	DIS3
Cell_Line	K562
Method	CRISPR
Exp_Name	DIS3-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	DIS3-BGKcLV46-21
Rep2	DIS3-BGKcLV46-22
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	63.2
Rep2_qPCR	55.2
Rep1_WB	81.8
Rep2_WB	85.2
Antibody Cat#	A303-764A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1638

Experiment Information (Status: Submitting)

	BGKcLV46-21	BGKcLV46-21	BGKcLV46-22	BGKcLV46-22
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0000925	BGC#0000925	BGC#0000925	BGC#0000925
shRNA_or_gRNA_sequence	GTGCTACCCACTGACTCTTG	GTGCTACCCACTGACTCTTG	GTGCTACCCACTGACTCTTG	GTGCTACCCACTGACTCTTG
PAM	GGG	GGG	GGG	GGG
Name	DIS3_86	DIS3_86	DIS3_86	DIS3_86
Sample_ID	BGKcLV46-21	BGKcLV46-21	BGKcLV46-22	BGKcLV46-22
transduction_Date	12/20/24	12/20/24	12/20/24	12/20/24
days	D6	D6	D6	D6
RBP_name	DIS3	DIS3	DIS3	DIS3
qPCR_result	63.2	63.2	55.2	55.2
Ave_qPCR	59.2	59.2
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3916	3916	3885	3885
WB_result	81.8	77.7	85.2	73.3858
Ave_WB
WB_DONE_date	12/31/24	1/13/25
MW	109KD
IP
antibody_Cat#	A303-764A	A303-765A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	6009	6011	6010	6012

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DIS3	Product_ID: A303-764A Lot_ID: 1 Source: Bethyl Labs Target Name: DIS3-human
DIS3	Product_ID: A303-765A Lot_ID: 1 Source: Bethyl Labs Target Name: DIS3-human

Experiment Status

	BGKcLV46-21	BGKcLV46-21	BGKcLV46-22	BGKcLV46-22
Sample_ID	BGKcLV46-21	BGKcLV46-21	BGKcLV46-22	BGKcLV46-22
Sample Name
Sample Name	DIS3-BGKcLV46-21		DIS3-BGKcLV46-22
RBP	DIS3	DIS3	DIS3	DIS3
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2025-04-21	2025-02-10	2025-04-21	2025-02-10
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14030	14084	14031	14085

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-21	BGKcLV46-22
Sample #	9	10
Sample Name	DIS3-BGKcLV46-21	DIS3-BGKcLV46-22
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	311	302
Peak_Molarity	36.90	80.90
libSampleQC_DNA_Well	DNA_Library_set77/set1/A8.png	DNA_Library_set77/set1/B8.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set77/set1/A2.png	RNA_Library_set77/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-21	BGKcLV46-22
RBP	DIS3	DIS3
Batch_ID	BGKcLV46	BGKcLV46
WB_result	81.800	85.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4668	4669

Sequencing Information

	BGKcLV46-21	BGKcLV46-22
Sample_ID	BGKcLV46-21	BGKcLV46-22
Sample Name	DIS3-BGKcLV46-21	DIS3-BGKcLV46-22
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	55,256,338	63,299,380
total_aligned_reads	51,306,412	58,309,491
unique_aligned_reads	47,130,358	53,720,607
percent_uniqueAligned	0.85294	0.84868
correlation_replicates	0.996554	0.996554
spikein_reads	147,174	156,970
percent_spikeins	0.00266	0.00248
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3373	3374

Data Submission Information DCC submission information was not avaliable

File Information

Search:

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
DIS3-BGKcLV46-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3373					GRCh38	V40	DIS3-BGKcLV46-21_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,DIS3-BGKcLV46-21_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32254
DIS3-BGKcLV46-21_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3373					GRCh38	V40	DIS3-BGKcLV46-21_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,DIS3-BGKcLV46-21_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32504
DIS3-BGKcLV46-21_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3373	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32154
DIS3-BGKcLV46-21_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3373	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32204
DIS3-BGKcLV46-21_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3373					GRCh38	V40	DIS3-BGKcLV46-21_Aligned.sortedByCoord.out.bam		ENCORE2	32454
DIS3-BGKcLV46-21_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3373					GRCh38	V40	DIS3-BGKcLV46-21_Aligned.sortedByCoord.out.bam		ENCORE2	32404
DIS3-BGKcLV46-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3373					GRCh38	V40	DIS3-BGKcLV46-21_Aligned.sortedByCoord.out.bam		ENCORE2	32354
DIS3-BGKcLV46-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3373					GRCh38	V40	DIS3-BGKcLV46-21_Aligned.sortedByCoord.out.bam		ENCORE2	32304
DIS3-BGKcLV46-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3374					GRCh38	V40	DIS3-BGKcLV46-22_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,DIS3-BGKcLV46-22_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32255
DIS3-BGKcLV46-22_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3374					GRCh38	V40	DIS3-BGKcLV46-22_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,DIS3-BGKcLV46-22_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32505
DIS3-BGKcLV46-22_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3374	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32155
DIS3-BGKcLV46-22_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3374	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32205
DIS3-BGKcLV46-22_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3374					GRCh38	V40	DIS3-BGKcLV46-22_Aligned.sortedByCoord.out.bam		ENCORE2	32455
DIS3-BGKcLV46-22_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3374					GRCh38	V40	DIS3-BGKcLV46-22_Aligned.sortedByCoord.out.bam		ENCORE2	32405
DIS3-BGKcLV46-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3374					GRCh38	V40	DIS3-BGKcLV46-22_Aligned.sortedByCoord.out.bam		ENCORE2	32355
DIS3-BGKcLV46-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3374					GRCh38	V40	DIS3-BGKcLV46-22_Aligned.sortedByCoord.out.bam		ENCORE2	32305

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