EXOSC10 RNA-Seq in HepG2

General Information


RBP	EXOSC10
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EXOSC10-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR590UTB
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR455KXW
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	EXOSC10-BGHcLV22-23
Rep2	EXOSC10-BGHcLV22-24
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	83.1
Rep2_WB	86.7
Antibody Cat#	A303-987A
Antibody Lot#	Lot# 1
Antibody DCC ID	ENCAB270KRD
Status	Released
Project	ENCODE4
ID	41

Experiment Information (Status: Released)

	BGHcLV22-23	BGHcLV22-24
idx	616	617
TRCN#_or_BGC#	BGC#0000516	BGC#0000516
shRNA_or_gRNA_sequence	TAATGTTGCTGCGACACCCA	TAATGTTGCTGCGACACCCA
PAM	TGG	TGG
Name	EXOSC10_93	EXOSC10_93
Sample_ID	BGHcLV22-23	BGHcLV22-24
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	EXOSC10	EXOSC10
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	TGAGCTGGAAGACAAGTTTGATT
RT-qPCR_primer-R	AGGGAGGACAGGCTGTTGAT
protein_conc	2525	2300
WB_result	83.1	86.7
Ave_WB	84.9
WB_DONE_date	9/4/20	JESS
MW	101kDa
IP	Rabbit / I
antibody_Cat#	A303-987A	Lot# 1
Antibody DCC ID	ENCAB270KRD
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	6771	6772

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EXOSC10	Product_ID: A303-987A Lot_ID: 1 Source: Bethyl Labs Target Name: EXOSC10-human

Experiment Status

	BGHcLV22-23	BGHcLV22-24
Sample_ID	BGHcLV22-23	BGHcLV22-24
Sample Name
Sample Name	EXOSC10-BGHcLV22-23	EXOSC10-BGHcLV22-24
RBP	EXOSC10	EXOSC10
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7375	7376

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-23	BGHcLV22-24
Sample #	11	12
Sample Name	EXOSC10-BGHcLV22-23	EXOSC10-BGHcLV22-24
Sample_Name_Alias
Index Well Position	C02	D02
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	338
Peak_Molarity	79.50	107.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/C2.png	DNA_Library_set46/set1/D2.png
RIN	9.4	9.7
libSample_RNA_Well	RNA_Library_set46/set1/C10.png	RNA_Library_set46/set1/D10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-23	BGHcLV22-24
RBP	EXOSC10	EXOSC10
Batch_ID	BGHcLV22	BGHcLV22
WB_result	83.100	86.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1386	1387

Sequencing Information

	BGHcLV22-23	BGHcLV22-24
Sample_ID	BGHcLV22-23	BGHcLV22-24
Sample Name	EXOSC10-BGHcLV22-23	EXOSC10-BGHcLV22-24
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	215,071,426	206,615,426
total_aligned_reads	188,385,924	185,192,474
unique_aligned_reads	176,409,838	173,236,028
percent_uniqueAligned	0.82024	0.83845
correlation_replicates	0.999540	0.999540
spikein_reads	99,678	66,570
percent_spikeins	0.00046	0.00032
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	492	493

Data Submission Information

	BGHcLV22-23	BGHcLV22-23	BGHcLV22-23	BGHcLV22-23	BGHcLV22-23	BGHcLV22-23	BGHcLV22-24	BGHcLV22-24	BGHcLV22-24	BGHcLV22-24
ENCODE_alias	brenton-graveley:EXOSC10-BGHcLV22	brenton-graveley:EXOSC10-BGHcLV22-23	brenton-graveley:L-EXOSC10-BGHcLV22-23	brenton-graveley:EXOSC10-BGHcLV22-23_TCTCTACT+GAACCGCG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EXOSC10-BGHcLV22-23_TCTCTACT+GAACCGCG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EXOSC10-BGHcLV22-HepG2	brenton-graveley:EXOSC10-BGHcLV22-24	brenton-graveley:L-EXOSC10-BGHcLV22-24	brenton-graveley:EXOSC10-BGHcLV22-24_CTCTCGTC+AGGTTATA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EXOSC10-BGHcLV22-24_CTCTCGTC+AGGTTATA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR455KXW	ENCBS673PHM	ENCLB510CAE	ENCFF262OZH	ENCFF213QGB	ENCSR590UTB	ENCBS802NJT	ENCLB753WQP	ENCFF435VEI	ENCFF902WLV
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	BGHcLV22-23	BGHcLV22-23	BGHcLV22-23	BGHcLV22-23	BGHcLV22-23	BGHcLV22-23	BGHcLV22-24	BGHcLV22-24	BGHcLV22-24	BGHcLV22-24
Sample Name	EXOSC10-BGHcLV22-23	EXOSC10-BGHcLV22-23	EXOSC10-BGHcLV22-23	EXOSC10-BGHcLV22-23	EXOSC10-BGHcLV22-23	EXOSC10-BGHcLV22-23	EXOSC10-BGHcLV22-24	EXOSC10-BGHcLV22-24	EXOSC10-BGHcLV22-24	EXOSC10-BGHcLV22-24
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	2022-03-04	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2022-03-04	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		EXOSC10-BGHcLV22-23.pdf	L-EXOSC10-BGHcLV22-23.pdf				EXOSC10-BGHcLV22-24.pdf	L-EXOSC10-BGHcLV22-24.pdf
ID	2400	2437	2501	2565	2595	7216	2438	2502	2566	2596

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
EXOSC10-BGHcLV22-23_TCTCTACT+GAACCGCG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	492	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	1356
EXOSC10-BGHcLV22-23_TCTCTACT+GAACCGCG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	492	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	1420
EXOSC10-BGHcLV22-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	492					GRCh38	V40	EXOSC10-BGHcLV22-23_TCTCTACT+GAACCGCG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC10-BGHcLV22-23_TCTCTACT+GAACCGCG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25259
EXOSC10-BGHcLV22-23_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	492					GRCh38	V40	EXOSC10-BGHcLV22-23_TCTCTACT+GAACCGCG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC10-BGHcLV22-23_TCTCTACT+GAACCGCG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25357
EXOSC10-BGHcLV22-23_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	492					GRCh38	V40	EXOSC10-BGHcLV22-23/Aligned.sortedByCoord.out.bam		ENCORE2	26007
EXOSC10-BGHcLV22-23_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	492					GRCh38	V40	EXOSC10-BGHcLV22-23/Aligned.sortedByCoord.out.bam		ENCORE2	26037
EXOSC10-BGHcLV22-23_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	492					GRCh38	V40	EXOSC10-BGHcLV22-23/Aligned.sortedByCoord.out.bam		ENCORE2	26067
EXOSC10-BGHcLV22-23_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	492					GRCh38	V40	EXOSC10-BGHcLV22-23/Aligned.sortedByCoord.out.bam		ENCORE2	26097
EXOSC10-BGHcLV22-24_CTCTCGTC+AGGTTATA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	493	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	1357
EXOSC10-BGHcLV22-24_CTCTCGTC+AGGTTATA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	493	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	1421
EXOSC10-BGHcLV22-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	493					GRCh38	V40	EXOSC10-BGHcLV22-24_CTCTCGTC+AGGTTATA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC10-BGHcLV22-24_CTCTCGTC+AGGTTATA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25260
EXOSC10-BGHcLV22-24_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	493					GRCh38	V40	EXOSC10-BGHcLV22-24_CTCTCGTC+AGGTTATA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC10-BGHcLV22-24_CTCTCGTC+AGGTTATA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25358
EXOSC10-BGHcLV22-24_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	493					GRCh38	V40	EXOSC10-BGHcLV22-24/Aligned.sortedByCoord.out.bam		ENCORE2	26008
EXOSC10-BGHcLV22-24_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	493					GRCh38	V40	EXOSC10-BGHcLV22-24/Aligned.sortedByCoord.out.bam		ENCORE2	26038
EXOSC10-BGHcLV22-24_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	493					GRCh38	V40	EXOSC10-BGHcLV22-24/Aligned.sortedByCoord.out.bam		ENCORE2	26068
EXOSC10-BGHcLV22-24_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	493					GRCh38	V40	EXOSC10-BGHcLV22-24/Aligned.sortedByCoord.out.bam		ENCORE2	26098