REXO2 RNA-Seq in K562

General Information


RBP	REXO2
Cell_Line	K562
Method	CRISPR
Exp_Name	REXO2-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	REXO2-BGKcLV46-55
Rep2	REXO2-BGKcLV46-56
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	27.7
Rep2_qPCR	33.2
Rep1_WB	56.7
Rep2_WB	64.9
Antibody Cat#	A304-812A
Antibody Lot#	lot# 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1646

Experiment Information (Status: Submitting)

	BGKcLV46-55	BGKcLV46-56
idx	0	0
TRCN#_or_BGC#	BGC#0001254	BGC#0001254
shRNA_or_gRNA_sequence	TGGTCCCGGGTGATGCTAGG	TGGTCCCGGGTGATGCTAGG
PAM	CGG	CGG
Name	REXO2_81	REXO2_81
Sample_ID	BGKcLV46-55	BGKcLV46-56
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	REXO2	REXO2
qPCR_result	27.7	33.2
Ave_qPCR	30.5
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3837	4389
WB_result	56.7	64.9
Ave_WB
WB_DONE_date	1/13/25,1/23/25
MW	27kd
IP
antibody_Cat#	A304-812A	lot# 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	6051	6052

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
REXO2	Product_ID: A304-812A Lot_ID: 3 Source: Bethyl Labs Target Name: REXO2-human

Experiment Status

	BGKcLV46-55	BGKcLV46-56
Sample_ID	BGKcLV46-55	BGKcLV46-56
Sample Name
Sample Name	REXO2-BGKcLV46-55	REXO2-BGKcLV46-56
RBP	REXO2	REXO2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14046	14047

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-55	BGKcLV46-56
Sample #	25	26
Sample Name	REXO2-BGKcLV46-55	REXO2-BGKcLV46-56
Sample_Name_Alias
Index Well Position	A04	B04
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	318	315
Peak_Molarity	70.90	50.90
libSampleQC_DNA_Well	DNA_Library_set77/set1/A10.png	DNA_Library_set77/set1/B10.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set77/set1/A4.png	RNA_Library_set77/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-55	BGKcLV46-56
RBP	REXO2	REXO2
Batch_ID	BGKcLV46	BGKcLV46
WB_result	56.700	64.883
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4684	4685

Sequencing Information

	BGKcLV46-55	BGKcLV46-56
Sample_ID	BGKcLV46-55	BGKcLV46-56
Sample Name	REXO2-BGKcLV46-55	REXO2-BGKcLV46-56
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	55,559,999	56,690,117
total_aligned_reads	51,787,775	52,982,619
unique_aligned_reads	47,883,396	48,865,075
percent_uniqueAligned	0.86183	0.86197
correlation_replicates	0.996905	0.996905
spikein_reads	118,358	99,470
percent_spikeins	0.00213	0.00175
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3389	3390

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
REXO2-BGKcLV46-55_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3389	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	32174
REXO2-BGKcLV46-55_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3389	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	32224
REXO2-BGKcLV46-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3389					GRCh38	V40	REXO2-BGKcLV46-55_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,REXO2-BGKcLV46-55_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32274
REXO2-BGKcLV46-55_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	3389					GRCh38	V40	REXO2-BGKcLV46-55_Aligned.sortedByCoord.out.bam		ENCORE2	32324
REXO2-BGKcLV46-55_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	3389					GRCh38	V40	REXO2-BGKcLV46-55_Aligned.sortedByCoord.out.bam		ENCORE2	32374
REXO2-BGKcLV46-55_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	3389					GRCh38	V40	REXO2-BGKcLV46-55_Aligned.sortedByCoord.out.bam		ENCORE2	32424
REXO2-BGKcLV46-55_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	3389					GRCh38	V40	REXO2-BGKcLV46-55_Aligned.sortedByCoord.out.bam		ENCORE2	32474
REXO2-BGKcLV46-55_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3389					GRCh38	V40	REXO2-BGKcLV46-55_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,REXO2-BGKcLV46-55_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32524
REXO2-BGKcLV46-56_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3390	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	32175
REXO2-BGKcLV46-56_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3390	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	32225
REXO2-BGKcLV46-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3390					GRCh38	V40	REXO2-BGKcLV46-56_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,REXO2-BGKcLV46-56_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32275
REXO2-BGKcLV46-56_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	3390					GRCh38	V40	REXO2-BGKcLV46-56_Aligned.sortedByCoord.out.bam		ENCORE2	32325
REXO2-BGKcLV46-56_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	3390					GRCh38	V40	REXO2-BGKcLV46-56_Aligned.sortedByCoord.out.bam		ENCORE2	32375
REXO2-BGKcLV46-56_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	3390					GRCh38	V40	REXO2-BGKcLV46-56_Aligned.sortedByCoord.out.bam		ENCORE2	32425
REXO2-BGKcLV46-56_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	3390					GRCh38	V40	REXO2-BGKcLV46-56_Aligned.sortedByCoord.out.bam		ENCORE2	32475
REXO2-BGKcLV46-56_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3390					GRCh38	V40	REXO2-BGKcLV46-56_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,REXO2-BGKcLV46-56_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32525