EXO1 RNA-Seq in K562

General Information


RBP	EXO1
Cell_Line	K562
Method	CRISPR
Exp_Name	EXO1-BGKcLV40-K562
ENCODE_series_ID
Batch_ID	BGKcLV40
Pool ID	Pool-231226
Local_Set_Name	set67
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EXO1-BGKcLV40-33
Rep2	EXO1-BGKcLV40-34
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	62.4
Rep2_qPCR	59.8
Rep1_WB	94.1
Rep2_WB	81.5
Antibody Cat#	A302-640A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1365

Experiment Information (Status: Submitting)

	BGKcLV40-33	BGKcLV40-33	BGKcLV40-34	BGKcLV40-34
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0000999	BGC#0000999	BGC#0000999	BGC#0000999
shRNA_or_gRNA_sequence	AAGCTCGAGAGTGTTTCACC	AAGCTCGAGAGTGTTTCACC	AAGCTCGAGAGTGTTTCACC	AAGCTCGAGAGTGTTTCACC
PAM	CGG	CGG	CGG	CGG
Name	EXO1_89	EXO1_89	EXO1_89	EXO1_89
Sample_ID	BGKcLV40-33	BGKcLV40-33	BGKcLV40-34	BGKcLV40-34
transduction_Date	10/31/23	10/31/23	10/31/23	10/31/23
days	D6	D6	D6	D6
RBP_name	EXO1	EXO1	EXO1	EXO1
qPCR_result	62.4		59.8
Ave_qPCR	61.1
RT-qPCR_primer-F	tgggattggattagcaaagg
RT-qPCR_primer-R	attgttggcccgaataaacc
protein_conc	3618	3618	3328	3328
WB_result	94.1	86.9	81.5	91.1173
Ave_WB	87.8	89.0
WB_DONE_date	11/15/23	12/7/23
MW	94kd	94kd
IP
antibody_Cat#	A302-640A	A302-639A	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date	1/4/24	1/4/24
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5708	5710	5709	5711

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EXO1	Product_ID: A302-640A Lot_ID: 1 Source: Bethyl Labs Target Name: EXO1-human
EXO1	Product_ID: A302-639A Lot_ID: 1 Source: Bethyl Labs Target Name: EXO1-human

Experiment Status

	BGKcLV40-33	BGKcLV40-33	BGKcLV40-34	BGKcLV40-34
Sample_ID	BGKcLV40-33	BGKcLV40-33	BGKcLV40-34	BGKcLV40-34
Sample Name
Sample Name	EXO1-BGKcLV40-33		EXO1-BGKcLV40-34
RBP	EXO1	EXO1	EXO1	EXO1
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2024-02-16	2023-12-15	2024-02-16	2023-12-15
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	12774	12818	12775	12819

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-33	BGKcLV40-34
Sample #	21	22
Sample Name	EXO1-BGKcLV40-33	EXO1-BGKcLV40-34
Sample_Name_Alias
Index Well Position	E03	F03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-12-19	2023-12-19
Lib_ID	Lib-231219	Lib-231219
Tecan_Location
Tecan
Tecan_date
Size_bp	291	288
Peak_Molarity	77.70	86.70
libSampleQC_DNA_Well	DNA_Library_set67/set1/E9.png	DNA_Library_set67/set1/F9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/E3.png	RNA_Library_set67/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-33	BGKcLV40-34
RBP	EXO1	EXO1
Batch_ID	BGKcLV40	BGKcLV40
WB_result	94.100	81.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4158	4159

Sequencing Information

	BGKcLV40-33	BGKcLV40-34
Sample_ID	BGKcLV40-33	BGKcLV40-34
Sample Name	EXO1-BGKcLV40-33	EXO1-BGKcLV40-34
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	44,004,597	20,257,808
total_aligned_reads	39,619,187	17,493,597
unique_aligned_reads	36,454,000	16,067,202
percent_uniqueAligned	0.82841	0.79314
correlation_replicates	0.994903	0.994903
spikein_reads	9,038	8,908
percent_spikeins	0.00021	0.00044
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2813	2814

Data Submission Information DCC submission information was not avaliable

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
EXO1-BGKcLV40-33_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2813	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28159
EXO1-BGKcLV40-33_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2813	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28203
EXO1-BGKcLV40-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2813					GRCh38	V40	EXO1-BGKcLV40-33_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXO1-BGKcLV40-33_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28247
EXO1-BGKcLV40-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2813					GRCh38	V40	EXO1-BGKcLV40-33/Aligned.sortedByCoord.out.bam		ENCORE2	28291
EXO1-BGKcLV40-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2813					GRCh38	V40	EXO1-BGKcLV40-33/Aligned.sortedByCoord.out.bam		ENCORE2	28335
EXO1-BGKcLV40-33_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2813					GRCh38	V40	EXO1-BGKcLV40-33/Aligned.sortedByCoord.out.bam		ENCORE2	28379
EXO1-BGKcLV40-33_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2813					GRCh38	V40	EXO1-BGKcLV40-33/Aligned.sortedByCoord.out.bam		ENCORE2	28423
EXO1-BGKcLV40-33_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2813					GRCh38	V40	EXO1-BGKcLV40-33_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXO1-BGKcLV40-33_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28467
EXO1-BGKcLV40-34_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2814	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28160
EXO1-BGKcLV40-34_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2814	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28204
EXO1-BGKcLV40-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2814					GRCh38	V40	EXO1-BGKcLV40-34_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXO1-BGKcLV40-34_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28248
EXO1-BGKcLV40-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2814					GRCh38	V40	EXO1-BGKcLV40-34/Aligned.sortedByCoord.out.bam		ENCORE2	28292
EXO1-BGKcLV40-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2814					GRCh38	V40	EXO1-BGKcLV40-34/Aligned.sortedByCoord.out.bam		ENCORE2	28336
EXO1-BGKcLV40-34_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2814					GRCh38	V40	EXO1-BGKcLV40-34/Aligned.sortedByCoord.out.bam		ENCORE2	28380
EXO1-BGKcLV40-34_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2814					GRCh38	V40	EXO1-BGKcLV40-34/Aligned.sortedByCoord.out.bam		ENCORE2	28424
EXO1-BGKcLV40-34_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2814					GRCh38	V40	EXO1-BGKcLV40-34_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXO1-BGKcLV40-34_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28468