EXOSC9 RNA-Seq in K562

General Information


RBP	EXOSC9
Cell_Line	K562
Method	shRNA
Exp_Name	EXOSC9-BGKLV13-K562
ENCODE_series_ID	ENCSR117YHI
Batch_ID	BGKLV13
Pool ID	Pool-140901
Local_Set_Name	set13
ENCODE_KD_Exp_ID	ENCSR812EIA
ENCODE_CN_Exp_ID	ENCSR815CVQ
Rep1	EXOSC9_BGKLV13_7
Rep2	EXOSC9_BGKLV13_8
CN1	NT_BGKLV13_1
CN2	NT_BGKLV13_2
Rep1_qPCR	72.3
Rep2_qPCR	73.4
Rep1_WB	31.8
Rep2_WB	20.5
Antibody Cat#	A303-888A
Antibody Lot#	A303-888A
Antibody DCC ID	ENCAB573YWT
Status	Released
Project	ENCODE3
ID	361

Experiment Information (Status: Released)

	BGKLV13-7	BGKLV13-8
idx	140	141
TRCN#_or_BGC#	TRCN0000050881	TRCN0000050881
shRNA_or_gRNA_sequence	CGTGTAGACCTACATTTATTA	CGTGTAGACCTACATTTATTA
PAM
Name	EXOSC9	EXOSC9
Sample_ID	BGKLV13-7	BGKLV13-8
transduction_Date	6/13/2014	6/13/2014
days
RBP_name	EXOSC9	EXOSC9
qPCR_result	72.3	73.4
Ave_qPCR	72.8
RT-qPCR_primer-F	ttgctgaagcagaacctcct
RT-qPCR_primer-R	ctctccaatttgggcagttc
protein_conc	2183	2088
WB_result	31.8	20.5
Ave_WB	26.2
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	72.871424	0
Rep2_TPM	48.5548457	0
Action
Library_start_date	7/27/2014	7/27/2014
repeat_library
Note
ID	155	156

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

	BGKLV13-7	BGKLV13-8
Sample_ID	BGKLV13-7	BGKLV13-8
Sample Name	EXOSC9_BGKLV13_7	EXOSC9_BGKLV13_8
Sample Name	EXOSC9_BGKLV13_7	EXOSC9_BGKLV13_8
RBP	EXOSC9	EXOSC9
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-10-29	2014-10-29
Project	ENCODE3	ENCODE3
Note
ID	448	449

Library-Prep
Sequencing

Library-Prep Information

	BGKLV13-7	BGKLV13-8
Sample #
Sample Name	EXOSC9-BGKLV13-7	EXOSC9-BGKLV13-8
Sample_Name_Alias	EXOSC9_BGKLV13_7	EXOSC9_BGKLV13_8
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-27	2014-07-27
Lib_ID	Lib-140727	Lib-140727
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/F1.png	DNA_Library_LV13-14/set1/G1.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_LV12/set1/A10.png	RNA_Library_LV12/set1/B10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV13-7	BGKLV13-8
RBP	EXOSC9	EXOSC9
Batch_ID	BGKLV13	BGKLV13
WB_result	31.800	20.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2124	2125

Sequencing Information

	BGKLV13-7	BGKLV13-8
Sample_ID	BGKLV13-7	BGKLV13-8
Sample Name	EXOSC9_BGKLV13_7	EXOSC9_BGKLV13_8
Pool ID	Pool-140901	Pool-140901
LocalServer_folder	set13	set13
total_reads	48,210,000	84,640,000
total_aligned_reads	44,210,694	78,806,836
unique_aligned_reads	40,724,600	72,420,086
percent_uniqueAligned	0.84473	0.85562
correlation_replicates	0.999258	0.999258
spikein_reads	324,934	385,654
percent_spikeins	0.00674	0.00456
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	766	767

Data Submission Information

	BGKLV13-7	BGKLV13-7
ENCODE_alias	brenton-graveley:EXOSC9_BGKLV13	brenton-graveley:EXOSC9-BGKLV13-K562
ENCODE_accession	ENCSR812EIA	ENCSR117YHI
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV13-7	BGKLV13-7
Sample Name	EXOSC9_BGKLV13_7	EXOSC9_BGKLV13_7
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2773	6705

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_BGKLV13_7_ACAGTG_L001_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	766	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13376
EXOSC9_BGKLV13_7_ACAGTG_L001_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	766	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13428
EXOSC9_BGKLV13_7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	766					GRCh38	V40	EXOSC9_BGKLV13_7_ACAGTG_L001_R1_001.fastq.gz,EXOSC9_BGKLV13_7_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	13480
EXOSC9_BGKLV13_7_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	766					GRCh38	V40	EXOSC9_BGKLV13_7/Aligned.sortedByCoord.out.bam		ENCORE2	13532
EXOSC9_BGKLV13_7_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	766					GRCh38	V40	EXOSC9_BGKLV13_7/Aligned.sortedByCoord.out.bam		ENCORE2	13584
EXOSC9_BGKLV13_7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	766					GRCh38	V40	EXOSC9_BGKLV13_7/Aligned.sortedByCoord.out.bam		ENCORE2	13636
EXOSC9_BGKLV13_7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	766					GRCh38	V40	EXOSC9_BGKLV13_7/Aligned.sortedByCoord.out.bam		ENCORE2	13688
EXOSC9_BGKLV13_7_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	766					GRCh38	V40	EXOSC9_BGKLV13_7_ACAGTG_L001_R1_001.fastq.gz,EXOSC9_BGKLV13_7_ACAGTG_L001_R2_001.fastq.gz		ENCORE2	13740
EXOSC9_BGKLV13_8_GCCAAT_L001_R1_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	767	HiSeq2000	100	paired-ended	1				NT_BGKLV13_1_ATCACG_L001_R1_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	13377
EXOSC9_BGKLV13_8_GCCAAT_L001_R2_001.fastq.gz	ENCODE_DATA/set13/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	767	HiSeq2000	100	paired-ended	2				NT_BGKLV13_1_ATCACG_L001_R2_001.fastq.gz,NT_BGKLV13_2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	13429
EXOSC9_BGKLV13_8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	767					GRCh38	V40	EXOSC9_BGKLV13_8_GCCAAT_L001_R1_001.fastq.gz,EXOSC9_BGKLV13_8_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	13481
EXOSC9_BGKLV13_8_Signal.Unique.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	767					GRCh38	V40	EXOSC9_BGKLV13_8/Aligned.sortedByCoord.out.bam		ENCORE2	13533
EXOSC9_BGKLV13_8_Signal.Unique.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	767					GRCh38	V40	EXOSC9_BGKLV13_8/Aligned.sortedByCoord.out.bam		ENCORE2	13585
EXOSC9_BGKLV13_8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	767					GRCh38	V40	EXOSC9_BGKLV13_8/Aligned.sortedByCoord.out.bam		ENCORE2	13637
EXOSC9_BGKLV13_8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set13/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	767					GRCh38	V40	EXOSC9_BGKLV13_8/Aligned.sortedByCoord.out.bam		ENCORE2	13689
EXOSC9_BGKLV13_8_quant.sf	ENCODE_DATA/set13/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	767					GRCh38	V40	EXOSC9_BGKLV13_8_GCCAAT_L001_R1_001.fastq.gz,EXOSC9_BGKLV13_8_GCCAAT_L001_R2_001.fastq.gz		ENCORE2	13741