REXO2 RNA-Seq in HepG2

General Information


RBP	REXO2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	REXO2-BGHcLV32-HepG2
ENCODE_series_ID	ENCSR030HWI
Batch_ID	BGHcLV32
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR199WMC
ENCODE_CN_Exp_ID	ENCSR232ERY
Rep1	REXO2-BGHcLV32-29
Rep2	REXO2-BGHcLV32-30
CN1	NT-BGHcLV32-1
CN2	NT-BGHcLV32-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	64.9
Rep2_WB	73.6
Antibody Cat#	A304-812A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB364BXM
Status	Submitted
Project	ENCODE4
ID	933

Experiment Information (Status: Released)

	BGHcLV32-29	BGHcLV32-30
idx	1028	1029
TRCN#_or_BGC#	BGC#0000779	BGC#0000779
shRNA_or_gRNA_sequence	CACGGACGGTTCGGGGCCCG	CACGGACGGTTCGGGGCCCG
PAM	AGG	AGG
Name	REXO2_83	REXO2_83
Sample_ID	BGHcLV32-29	BGHcLV32-30
transduction_Date	10/28/21	10/28/21
days	D6	D6
RBP_name	REXO2	REXO2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ttacattgcagcaggcagag
RT-qPCR_primer-R	tggggcatgtatttgtcaag
protein_conc	4596	4425
WB_result	64.9	73.6
Ave_WB	69.3
WB_DONE_date	12/15/21
MW	27KD
IP
antibody_Cat#	A304-812A	LOT #1
Antibody DCC ID	ENCAB364BXM	8/4/22
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	2/9/22	2/9/22
repeat_library
Note
ID	7207	7208

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
REXO2	Product_ID: A304-812A Lot_ID: 1 Source: Bethyl Labs Target Name: REXO2-human

Experiment Status

	BGHcLV32-29	BGHcLV32-30
Sample_ID	BGHcLV32-29	BGHcLV32-30
Sample Name
Sample Name	REXO2-BGHcLV32-29	REXO2-BGHcLV32-30
RBP	REXO2	REXO2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10363	10364

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV32-29	BGHcLV32-30
Sample #	37	38
Sample Name	REXO2-BGHcLV32-29	REXO2-BGHcLV32-30
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-02-01	2022-02-01
Lib_ID	Lib-220201	Lib-220201
Tecan_Location
Tecan
Tecan_date
Size_bp	311	295
Peak_Molarity	74.40	52.50
libSampleQC_DNA_Well	DNA_Library_set52/set2/E5.png	DNA_Library_set52/set2/F5.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set52/set2/A8.png	RNA_Library_set52/set2/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-02-16	2022-02-16
Sample_ID	BGHcLV32-29	BGHcLV32-30
RBP	REXO2	REXO2
Batch_ID	BGHcLV32	BGHcLV32
WB_result	64.900	73.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3214	3215

Sequencing Information

	BGHcLV32-29	BGHcLV32-30
Sample_ID	BGHcLV32-29	BGHcLV32-30
Sample Name	REXO2-BGHcLV32-29	REXO2-BGHcLV32-30
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	158,729,084	143,312,974
total_aligned_reads	131,671,774	123,574,636
unique_aligned_reads	123,695,942	115,813,064
percent_uniqueAligned	0.77929	0.80811
correlation_replicates	0.994479	0.994479
spikein_reads	13,552	12,842
percent_spikeins	0.00009	0.00009
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2011	2012

Data Submission Information

	BGHcLV32-29	BGHcLV32-29	BGHcLV32-29	BGHcLV32-29	BGHcLV32-29	BGHcLV32-29	BGHcLV32-30	BGHcLV32-30	BGHcLV32-30	BGHcLV32-30
ENCODE_alias	brenton-graveley:REXO2-BGHcLV32	brenton-graveley:REXO2-BGHcLV32-29	brenton-graveley:L-REXO2-BGHcLV32-29	brenton-graveley:REXO2-BGHcLV32-29_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:REXO2-BGHcLV32-29_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:REXO2-BGHcLV32-HepG2	brenton-graveley:REXO2-BGHcLV32-30	brenton-graveley:L-REXO2-BGHcLV32-30	brenton-graveley:REXO2-BGHcLV32-30_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:REXO2-BGHcLV32-30_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR199WMC	ENCBS727HEC	ENCLB217NFR	ENCFF445KIK	ENCFF601DSQ	ENCSR030HWI	ENCBS897RMB	ENCLB509UKE	ENCFF134KKX	ENCFF846EJD
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	BGHcLV32-29	BGHcLV32-29	BGHcLV32-29	BGHcLV32-29	BGHcLV32-29	BGHcLV32-29	BGHcLV32-30	BGHcLV32-30	BGHcLV32-30	BGHcLV32-30
Sample Name	REXO2-BGHcLV32-29	REXO2-BGHcLV32-29	REXO2-BGHcLV32-29	REXO2-BGHcLV32-29	REXO2-BGHcLV32-29	REXO2-BGHcLV32-29	REXO2-BGHcLV32-30	REXO2-BGHcLV32-30	REXO2-BGHcLV32-30	REXO2-BGHcLV32-30
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV52_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		REXO2-BGHcLV32-29.pdf	L-REXO2-BGHcLV32-29.pdf				REXO2-BGHcLV32-30.pdf	L-REXO2-BGHcLV32-30.pdf
ID	7463	7533	7645	7753	7863	7953	7534	7646	7754	7864

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-BGHcLV32-29_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2011	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6509
REXO2-BGHcLV32-29_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2011	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6563
REXO2-BGHcLV32-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2011					GRCh38	V40	REXO2-BGHcLV32-29_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,REXO2-BGHcLV32-29_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18430
REXO2-BGHcLV32-29_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2011					GRCh38	V40	REXO2-BGHcLV32-29/Aligned.sortedByCoord.out.bam		ENCORE2	18484
REXO2-BGHcLV32-29_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2011					GRCh38	V40	REXO2-BGHcLV32-29/Aligned.sortedByCoord.out.bam		ENCORE2	18538
REXO2-BGHcLV32-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2011					GRCh38	V40	REXO2-BGHcLV32-29/Aligned.sortedByCoord.out.bam		ENCORE2	18592
REXO2-BGHcLV32-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2011					GRCh38	V40	REXO2-BGHcLV32-29/Aligned.sortedByCoord.out.bam		ENCORE2	18646
REXO2-BGHcLV32-29_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2011					GRCh38	V40	REXO2-BGHcLV32-29_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,REXO2-BGHcLV32-29_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18700
REXO2-BGHcLV32-30_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2012	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6510
REXO2-BGHcLV32-30_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2012	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6564
REXO2-BGHcLV32-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2012					GRCh38	V40	REXO2-BGHcLV32-30_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,REXO2-BGHcLV32-30_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18431
REXO2-BGHcLV32-30_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2012					GRCh38	V40	REXO2-BGHcLV32-30/Aligned.sortedByCoord.out.bam		ENCORE2	18485
REXO2-BGHcLV32-30_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2012					GRCh38	V40	REXO2-BGHcLV32-30/Aligned.sortedByCoord.out.bam		ENCORE2	18539
REXO2-BGHcLV32-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2012					GRCh38	V40	REXO2-BGHcLV32-30/Aligned.sortedByCoord.out.bam		ENCORE2	18593
REXO2-BGHcLV32-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2012					GRCh38	V40	REXO2-BGHcLV32-30/Aligned.sortedByCoord.out.bam		ENCORE2	18647
REXO2-BGHcLV32-30_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2012					GRCh38	V40	REXO2-BGHcLV32-30_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,REXO2-BGHcLV32-30_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18701