EXOSC9 RNA-Seq in HepG2

General Information


RBP	EXOSC9
Cell_Line	HepG2
Method	shRNA
Exp_Name	EXOSC9-BGHLV14-HepG2
ENCODE_series_ID	ENCSR379WHE
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR597IYB
ENCODE_CN_Exp_ID	ENCSR003EKR
Rep1	EXOSC9_BGHLV14-17
Rep2	EXOSC9_BGHLV14-18
CN1	NT_BGHLV14-1_1
CN2	NT_BGHLV14-2_1
Rep1_qPCR	66.8
Rep2_qPCR	67.1
Rep1_WB	52.2
Rep2_WB	59.6
Antibody Cat#	A303-888A
Antibody Lot#	A303-888A
Antibody DCC ID	ENCAB573YWT
Status	Released
Project	ENCODE3
ID	391

Experiment Information (Status: Released)

	BGHLV14-17	BGHLV14-18
idx	113	114
TRCN#_or_BGC#	TRCN0000050881	TRCN0000050881
shRNA_or_gRNA_sequence	CGTGTAGACCTACATTTATTA	CGTGTAGACCTACATTTATTA
PAM
Name	EXOSC9	EXOSC9
Sample_ID	BGHLV14-17	BGHLV14-18
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	EXOSC9	EXOSC9
qPCR_result	66.8	67.1
Ave_qPCR	67.0
RT-qPCR_primer-F	ttgctgaagcagaacctcct
RT-qPCR_primer-R	ctctccaatttgggcagttc
protein_conc	4855	4806
WB_result	52.2	59.6
Ave_WB	55.9
WB_DONE_date	7/30/2014
MW	49kDa
IP	1MW	1MW
antibody_Cat#	A303-888A	A303-888A
Antibody DCC ID	ENCAB573YWT	ENCAB573YWT
submitted_to_DCC_date	5/4/2015
Rep1_TPM	25.3	0
Rep2_TPM	18.8	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	2170	2171

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EXOSC9	Product_ID: A303-888A Lot_ID: 1 Source: Bethyl Labs Target Name: EXOSC9-human

Experiment Status

	BGHLV14-17	BGHLV14-18
Sample_ID	BGHLV14-17	BGHLV14-18
Sample Name	EXOSC9_BGHLV14-17	EXOSC9_BGHLV14-18
Sample Name	EXOSC9_BGHLV14-17	EXOSC9_BGHLV14-18
RBP	EXOSC9	EXOSC9
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	504	505

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-17	BGHLV14-18
Sample #
Sample Name	EXOSC9-BGHLV14-17	EXOSC9-BGHLV14-18
Sample_Name_Alias	EXOSC9_BGHLV14-17	EXOSC9_BGHLV14-18
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/F9.png	DNA_Library_LV13-14/set1/G9.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/A6.png	RNA_Library_LV13-14-16/set1/B6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-17	BGHLV14-18
RBP	EXOSC9	EXOSC9
Batch_ID	BGHLV14	BGHLV14
WB_result	52.200	59.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2188	2189

Sequencing Information

	BGHLV14-17	BGHLV14-18
Sample_ID	BGHLV14-17	BGHLV14-18
Sample Name	EXOSC9_BGHLV14-17	EXOSC9_BGHLV14-18
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	44,000,000	47,160,000
total_aligned_reads	41,536,286	44,524,138
unique_aligned_reads	39,083,582	41,851,086
percent_uniqueAligned	0.88826	0.88743
correlation_replicates	0.996203	0.996203
spikein_reads	168,292	207,578
percent_spikeins	0.00382	0.00440
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	830	831

Data Submission Information

	BGHLV14-17	BGHLV14-17
ENCODE_alias	brenton-graveley:EXOSC9_BGHLV14	brenton-graveley:EXOSC9-BGHLV14-HepG2
ENCODE_accession	ENCSR597IYB	ENCSR379WHE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-17	BGHLV14-17
Sample Name	EXOSC9_BGHLV14-17	EXOSC9_BGHLV14-17
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2802	6704

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
EXOSC9_BGHLV14-17_CGTACG_L002_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	830	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13796
EXOSC9_BGHLV14-17_CGTACG_L002_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	830	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13858
EXOSC9_BGHLV14-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	830					GRCh38	V40	EXOSC9_BGHLV14-17_CGTACG_L002_R1_001.fastq.gz,EXOSC9_BGHLV14-17_CGTACG_L002_R2_001.fastq.gz		ENCORE2	13920
EXOSC9_BGHLV14-17_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	830					GRCh38	V40	EXOSC9_BGHLV14-17/Aligned.sortedByCoord.out.bam		ENCORE2	13982
EXOSC9_BGHLV14-17_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	830					GRCh38	V40	EXOSC9_BGHLV14-17/Aligned.sortedByCoord.out.bam		ENCORE2	14044
EXOSC9_BGHLV14-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	830					GRCh38	V40	EXOSC9_BGHLV14-17/Aligned.sortedByCoord.out.bam		ENCORE2	14106
EXOSC9_BGHLV14-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	830					GRCh38	V40	EXOSC9_BGHLV14-17/Aligned.sortedByCoord.out.bam		ENCORE2	14168
EXOSC9_BGHLV14-17_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	830					GRCh38	V40	EXOSC9_BGHLV14-17_CGTACG_L002_R1_001.fastq.gz,EXOSC9_BGHLV14-17_CGTACG_L002_R2_001.fastq.gz		ENCORE2	14230
EXOSC9_BGHLV14-18_GAGTGG_L002_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	831	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13797
EXOSC9_BGHLV14-18_GAGTGG_L002_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	831	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13859
EXOSC9_BGHLV14-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	831					GRCh38	V40	EXOSC9_BGHLV14-18_GAGTGG_L002_R1_001.fastq.gz,EXOSC9_BGHLV14-18_GAGTGG_L002_R2_001.fastq.gz		ENCORE2	13921
EXOSC9_BGHLV14-18_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	831					GRCh38	V40	EXOSC9_BGHLV14-18/Aligned.sortedByCoord.out.bam		ENCORE2	13983
EXOSC9_BGHLV14-18_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	831					GRCh38	V40	EXOSC9_BGHLV14-18/Aligned.sortedByCoord.out.bam		ENCORE2	14045
EXOSC9_BGHLV14-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	831					GRCh38	V40	EXOSC9_BGHLV14-18/Aligned.sortedByCoord.out.bam		ENCORE2	14107
EXOSC9_BGHLV14-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	831					GRCh38	V40	EXOSC9_BGHLV14-18/Aligned.sortedByCoord.out.bam		ENCORE2	14169
EXOSC9_BGHLV14-18_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	831					GRCh38	V40	EXOSC9_BGHLV14-18_GAGTGG_L002_R1_001.fastq.gz,EXOSC9_BGHLV14-18_GAGTGG_L002_R2_001.fastq.gz		ENCORE2	14231