EXOSC2 RNA-Seq in HepG2

General Information


RBP	EXOSC2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EXOSC2-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR775GQL
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR035LEO
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	EXOSC2-BGHcLV22-25
Rep2	EXOSC2-BGHcLV22-26
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	71.1
Rep2_WB	64.2
Antibody Cat#	A303-886A
Antibody Lot#	lot# 1
Antibody DCC ID	ENCAB374YDD
Status	Released
Project	ENCODE4
ID	42

Experiment Information (Status: Released)

	BGHcLV22-25	BGHcLV22-26
idx	618	619
TRCN#_or_BGC#	BGC#0000517	BGC#0000517
shRNA_or_gRNA_sequence	GAAACATCTAGTGGTGCCGG	GAAACATCTAGTGGTGCCGG
PAM	GGG	GGG
Name	EXOSC2_90	EXOSC2_90
Sample_ID	BGHcLV22-25	BGHcLV22-26
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	EXOSC2	EXOSC2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	CCTGCACTGGCTGATTTCAT
RT-qPCR_primer-R	TGCATCTGCTGGGGTAAAGT
protein_conc	2567	2124
WB_result	71.1	64.2
Ave_WB	67.7
WB_DONE_date	9/2/20	JESS
MW	32.8kDa
IP	Rabbit / I
antibody_Cat#	A303-886A	lot# 1
Antibody DCC ID	ENCAB374YDD
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	6773	6774

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EXOSC2	Product_ID: A303-886A Lot_ID: 1 Source: Bethyl Labs Target Name: EXOSC2-human

Experiment Status

	BGHcLV22-25	BGHcLV22-26
Sample_ID	BGHcLV22-25	BGHcLV22-26
Sample Name
Sample Name	EXOSC2-BGHcLV22-25	EXOSC2-BGHcLV22-26
RBP	EXOSC2	EXOSC2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7377	7378

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-25	BGHcLV22-26
Sample #	13	14
Sample Name	EXOSC2-BGHcLV22-25	EXOSC2-BGHcLV22-26
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	289	296
Peak_Molarity	110.00	134.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/E2.png	DNA_Library_set46/set1/F2.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set46/set1/E10.png	RNA_Library_set46/set1/F10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-25	BGHcLV22-26
RBP	EXOSC2	EXOSC2
Batch_ID	BGHcLV22	BGHcLV22
WB_result	71.100	64.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1388	1389

Sequencing Information

	BGHcLV22-25	BGHcLV22-26
Sample_ID	BGHcLV22-25	BGHcLV22-26
Sample Name	EXOSC2-BGHcLV22-25	EXOSC2-BGHcLV22-26
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	179,895,092	121,549,774
total_aligned_reads	152,181,308	108,286,540
unique_aligned_reads	142,367,278	101,414,592
percent_uniqueAligned	0.79139	0.83435
correlation_replicates	0.975376	0.975376
spikein_reads	55,412	44,030
percent_spikeins	0.00031	0.00036
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	494	495

Data Submission Information

	BGHcLV22-25	BGHcLV22-25	BGHcLV22-25	BGHcLV22-25	BGHcLV22-25	BGHcLV22-25	BGHcLV22-26	BGHcLV22-26	BGHcLV22-26	BGHcLV22-26
ENCODE_alias	brenton-graveley:EXOSC2-BGHcLV22	brenton-graveley:EXOSC2-BGHcLV22-25	brenton-graveley:L-EXOSC2-BGHcLV22-25	brenton-graveley:EXOSC2-BGHcLV22-25_CCAAGTCT+TCATCCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EXOSC2-BGHcLV22-25_CCAAGTCT+TCATCCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EXOSC2-BGHcLV22-HepG2	brenton-graveley:EXOSC2-BGHcLV22-26	brenton-graveley:L-EXOSC2-BGHcLV22-26	brenton-graveley:EXOSC2-BGHcLV22-26_TTGGACTC+CTGCTTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EXOSC2-BGHcLV22-26_TTGGACTC+CTGCTTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR035LEO	ENCBS470ESE	ENCLB728OVD	ENCFF810ZJT	ENCFF413CPJ	ENCSR775GQL	ENCBS744VDF	ENCLB497XOZ	ENCFF293ERB	ENCFF342AOR
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	BGHcLV22-25	BGHcLV22-25	BGHcLV22-25	BGHcLV22-25	BGHcLV22-25	BGHcLV22-25	BGHcLV22-26	BGHcLV22-26	BGHcLV22-26	BGHcLV22-26
Sample Name	EXOSC2-BGHcLV22-25	EXOSC2-BGHcLV22-25	EXOSC2-BGHcLV22-25	EXOSC2-BGHcLV22-25	EXOSC2-BGHcLV22-25	EXOSC2-BGHcLV22-25	EXOSC2-BGHcLV22-26	EXOSC2-BGHcLV22-26	EXOSC2-BGHcLV22-26	EXOSC2-BGHcLV22-26
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		EXOSC2-BGHcLV22-25.pdf	L-EXOSC2-BGHcLV22-25.pdf				EXOSC2-BGHcLV22-26.pdf	L-EXOSC2-BGHcLV22-26.pdf
ID	2401	2439	2503	2567	2597	7218	2440	2504	2568	2598

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
EXOSC2-BGHcLV22-25_CCAAGTCT+TCATCCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	494	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1358
EXOSC2-BGHcLV22-25_CCAAGTCT+TCATCCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	494	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1422
EXOSC2-BGHcLV22-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	494					GRCh38	V40	EXOSC2-BGHcLV22-25_CCAAGTCT+TCATCCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC2-BGHcLV22-25_CCAAGTCT+TCATCCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25261
EXOSC2-BGHcLV22-25_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	494					GRCh38	V40	EXOSC2-BGHcLV22-25_CCAAGTCT+TCATCCTT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC2-BGHcLV22-25_CCAAGTCT+TCATCCTT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25359
EXOSC2-BGHcLV22-25_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	494					GRCh38	V40	EXOSC2-BGHcLV22-25/Aligned.sortedByCoord.out.bam		ENCORE2	26009
EXOSC2-BGHcLV22-25_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	494					GRCh38	V40	EXOSC2-BGHcLV22-25/Aligned.sortedByCoord.out.bam		ENCORE2	26039
EXOSC2-BGHcLV22-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	494					GRCh38	V40	EXOSC2-BGHcLV22-25/Aligned.sortedByCoord.out.bam		ENCORE2	26069
EXOSC2-BGHcLV22-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	494					GRCh38	V40	EXOSC2-BGHcLV22-25/Aligned.sortedByCoord.out.bam		ENCORE2	26099
EXOSC2-BGHcLV22-26_TTGGACTC+CTGCTTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	495	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1359
EXOSC2-BGHcLV22-26_TTGGACTC+CTGCTTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	495	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1423
EXOSC2-BGHcLV22-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	495					GRCh38	V40	EXOSC2-BGHcLV22-26_TTGGACTC+CTGCTTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC2-BGHcLV22-26_TTGGACTC+CTGCTTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25262
EXOSC2-BGHcLV22-26_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	495					GRCh38	V40	EXOSC2-BGHcLV22-26_TTGGACTC+CTGCTTCC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC2-BGHcLV22-26_TTGGACTC+CTGCTTCC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25360
EXOSC2-BGHcLV22-26_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	495					GRCh38	V40	EXOSC2-BGHcLV22-26/Aligned.sortedByCoord.out.bam		ENCORE2	26010
EXOSC2-BGHcLV22-26_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	495					GRCh38	V40	EXOSC2-BGHcLV22-26/Aligned.sortedByCoord.out.bam		ENCORE2	26040
EXOSC2-BGHcLV22-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	495					GRCh38	V40	EXOSC2-BGHcLV22-26/Aligned.sortedByCoord.out.bam		ENCORE2	26070
EXOSC2-BGHcLV22-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	495					GRCh38	V40	EXOSC2-BGHcLV22-26/Aligned.sortedByCoord.out.bam		ENCORE2	26100