EXOSC9 RNA-Seq in K562

General Information


RBP	EXOSC9
Cell_Line	K562
Method	CRISPR
Exp_Name	EXOSC9-BGKcLV40-K562
ENCODE_series_ID
Batch_ID	BGKcLV40
Pool ID	Pool-231226
Local_Set_Name	set67
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EXOSC9-BGKcLV40-39
Rep2	EXOSC9-BGKcLV40-40
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	65.6
Rep2_qPCR	76.4
Rep1_WB	71.6
Rep2_WB	71.0
Antibody Cat#	A303-888A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1367

Experiment Information (Status: Submitting)

	BGKcLV40-39	BGKcLV40-40
idx	0	0
TRCN#_or_BGC#	BGC#0001005	BGC#0001005
shRNA_or_gRNA_sequence	GGTGAAGTTGAATCGACTCA	GGTGAAGTTGAATCGACTCA
PAM	TGG	TGG
Name	EXOSC9_90	EXOSC9_90
Sample_ID	BGKcLV40-39	BGKcLV40-40
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	EXOSC9	EXOSC9
qPCR_result	65.6	76.4
Ave_qPCR	71.0
RT-qPCR_primer-F	ttgctgaagcagaacctcct
RT-qPCR_primer-R	ctctccaatttgggcagttc
protein_conc	4288	4692
WB_result	71.6	71.0
Ave_WB	71.3
WB_DONE_date	11/17/23
MW	49kd
IP
antibody_Cat#	A303-888A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	1/4/24
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5716	5717

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

	BGKcLV40-39	BGKcLV40-40
Sample_ID	BGKcLV40-39	BGKcLV40-40
Sample Name
Sample Name	EXOSC9-BGKcLV40-39	EXOSC9-BGKcLV40-40
RBP	EXOSC9	EXOSC9
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12778	12779

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-39	BGKcLV40-40
Sample #	25	26
Sample Name	EXOSC9-BGKcLV40-39	EXOSC9-BGKcLV40-40
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-12-19	2023-12-19
Lib_ID	Lib-231219	Lib-231219
Tecan_Location
Tecan
Tecan_date
Size_bp	288	282
Peak_Molarity	60.10	45.60
libSampleQC_DNA_Well	DNA_Library_set67/set1/A10.png	DNA_Library_set67/set1/B10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/A4.png	RNA_Library_set67/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-39	BGKcLV40-40
RBP	EXOSC9	EXOSC9
Batch_ID	BGKcLV40	BGKcLV40
WB_result	71.600	71.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4162	4163

Sequencing Information

	BGKcLV40-39	BGKcLV40-40
Sample_ID	BGKcLV40-39	BGKcLV40-40
Sample Name	EXOSC9-BGKcLV40-39	EXOSC9-BGKcLV40-40
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	24,950,367	21,496,083
total_aligned_reads	21,106,076	17,715,415
unique_aligned_reads	19,404,819	16,286,507
percent_uniqueAligned	0.77774	0.75765
correlation_replicates	0.997857	0.997857
spikein_reads	4,526	1,802
percent_spikeins	0.00018	0.00008
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2817	2818

Data Submission Information DCC submission information was not avaliable

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-BGKcLV40-39_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2817	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28163
EXOSC9-BGKcLV40-39_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2817	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28207
EXOSC9-BGKcLV40-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2817					GRCh38	V40	EXOSC9-BGKcLV40-39_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC9-BGKcLV40-39_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28251
EXOSC9-BGKcLV40-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2817					GRCh38	V40	EXOSC9-BGKcLV40-39/Aligned.sortedByCoord.out.bam		ENCORE2	28295
EXOSC9-BGKcLV40-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2817					GRCh38	V40	EXOSC9-BGKcLV40-39/Aligned.sortedByCoord.out.bam		ENCORE2	28339
EXOSC9-BGKcLV40-39_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2817					GRCh38	V40	EXOSC9-BGKcLV40-39/Aligned.sortedByCoord.out.bam		ENCORE2	28383
EXOSC9-BGKcLV40-39_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2817					GRCh38	V40	EXOSC9-BGKcLV40-39/Aligned.sortedByCoord.out.bam		ENCORE2	28427
EXOSC9-BGKcLV40-39_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2817					GRCh38	V40	EXOSC9-BGKcLV40-39_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC9-BGKcLV40-39_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28471
EXOSC9-BGKcLV40-40_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2818	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28164
EXOSC9-BGKcLV40-40_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2818	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28208
EXOSC9-BGKcLV40-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2818					GRCh38	V40	EXOSC9-BGKcLV40-40_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC9-BGKcLV40-40_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28252
EXOSC9-BGKcLV40-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2818					GRCh38	V40	EXOSC9-BGKcLV40-40/Aligned.sortedByCoord.out.bam		ENCORE2	28296
EXOSC9-BGKcLV40-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2818					GRCh38	V40	EXOSC9-BGKcLV40-40/Aligned.sortedByCoord.out.bam		ENCORE2	28340
EXOSC9-BGKcLV40-40_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2818					GRCh38	V40	EXOSC9-BGKcLV40-40/Aligned.sortedByCoord.out.bam		ENCORE2	28384
EXOSC9-BGKcLV40-40_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2818					GRCh38	V40	EXOSC9-BGKcLV40-40/Aligned.sortedByCoord.out.bam		ENCORE2	28428
EXOSC9-BGKcLV40-40_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2818					GRCh38	V40	EXOSC9-BGKcLV40-40_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC9-BGKcLV40-40_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28472