EXOSC1 RNA-Seq in K562

General Information


RBP	EXOSC1
Cell_Line	K562
Method	CRISPR
Exp_Name	EXOSC1-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	EXOSC1-BGKcLV40-35
Rep2	EXOSC1-BGKcLV40-36
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	63.4
Rep2_qPCR	64.4
Rep1_WB	54.5
Rep2_WB	51.3
Antibody Cat#	A303-885A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1366

Experiment Information (Status: Submitting)

	BGKcLV40-35	BGKcLV40-36
idx	0	0
TRCN#_or_BGC#	BGC#0001000	BGC#0001000
shRNA_or_gRNA_sequence	AAGTACACATCCTGTATGTG	AAGTACACATCCTGTATGTG
PAM	GGG	GGG
Name	EXOSC1_74	EXOSC1_74
Sample_ID	BGKcLV40-35	BGKcLV40-36
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	EXOSC1	EXOSC1
qPCR_result	63.4	64.4
Ave_qPCR	63.9
RT-qPCR_primer-F	gagtggtggtagcccacagt
RT-qPCR_primer-R	tagggcactgcatctcacac
protein_conc	3872	4457
WB_result	54.5	51.3
Ave_WB	52.9
WB_DONE_date	11/8/23
MW	21kd
IP
antibody_Cat#	A303-885A	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	5712	5713

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EXOSC1	Product_ID: A303-885A Lot_ID: 1 Source: Bethyl Labs Target Name: EXOSC1-human

Experiment Status

	BGKcLV40-35	BGKcLV40-36
Sample_ID	BGKcLV40-35	BGKcLV40-36
Sample Name
Sample Name	EXOSC1-BGKcLV40-35	EXOSC1-BGKcLV40-36
RBP	EXOSC1	EXOSC1
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12776	12777

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-35	BGKcLV40-36
Sample #	23	24
Sample Name	EXOSC1-BGKcLV40-35	EXOSC1-BGKcLV40-36
Sample_Name_Alias
Index Well Position	G03	H03
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	281	290
Peak_Molarity	77.90	80.60
libSampleQC_DNA_Well	DNA_Library_set67/set1/G9.png	DNA_Library_set67/set1/H9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/G3.png	RNA_Library_set67/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-35	BGKcLV40-36
RBP	EXOSC1	EXOSC1
Batch_ID	BGKcLV40	BGKcLV40
WB_result	54.500	51.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4160	4161

Sequencing Information

	BGKcLV40-35	BGKcLV40-36
Sample_ID	BGKcLV40-35	BGKcLV40-36
Sample Name	EXOSC1-BGKcLV40-35	EXOSC1-BGKcLV40-36
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	24,913,292	23,113,353
total_aligned_reads	21,985,167	20,889,006
unique_aligned_reads	20,170,824	19,210,074
percent_uniqueAligned	0.80964	0.83112
correlation_replicates	0.992296	0.992296
spikein_reads	4,490	7,256
percent_spikeins	0.00018	0.00031
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2815	2816

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
EXOSC1-BGKcLV40-35_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2815	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	28161
EXOSC1-BGKcLV40-35_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2815	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	28205
EXOSC1-BGKcLV40-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2815					GRCh38	V40	EXOSC1-BGKcLV40-35_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC1-BGKcLV40-35_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28249
EXOSC1-BGKcLV40-35_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	2815					GRCh38	V40	EXOSC1-BGKcLV40-35/Aligned.sortedByCoord.out.bam		ENCORE2	28293
EXOSC1-BGKcLV40-35_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	2815					GRCh38	V40	EXOSC1-BGKcLV40-35/Aligned.sortedByCoord.out.bam		ENCORE2	28337
EXOSC1-BGKcLV40-35_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	2815					GRCh38	V40	EXOSC1-BGKcLV40-35/Aligned.sortedByCoord.out.bam		ENCORE2	28381
EXOSC1-BGKcLV40-35_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	2815					GRCh38	V40	EXOSC1-BGKcLV40-35/Aligned.sortedByCoord.out.bam		ENCORE2	28425
EXOSC1-BGKcLV40-35_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2815					GRCh38	V40	EXOSC1-BGKcLV40-35_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC1-BGKcLV40-35_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28469
EXOSC1-BGKcLV40-36_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2816	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	28162
EXOSC1-BGKcLV40-36_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2816	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	28206
EXOSC1-BGKcLV40-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2816					GRCh38	V40	EXOSC1-BGKcLV40-36_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC1-BGKcLV40-36_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28250
EXOSC1-BGKcLV40-36_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	2816					GRCh38	V40	EXOSC1-BGKcLV40-36/Aligned.sortedByCoord.out.bam		ENCORE2	28294
EXOSC1-BGKcLV40-36_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	2816					GRCh38	V40	EXOSC1-BGKcLV40-36/Aligned.sortedByCoord.out.bam		ENCORE2	28338
EXOSC1-BGKcLV40-36_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	2816					GRCh38	V40	EXOSC1-BGKcLV40-36/Aligned.sortedByCoord.out.bam		ENCORE2	28382
EXOSC1-BGKcLV40-36_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	2816					GRCh38	V40	EXOSC1-BGKcLV40-36/Aligned.sortedByCoord.out.bam		ENCORE2	28426
EXOSC1-BGKcLV40-36_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2816					GRCh38	V40	EXOSC1-BGKcLV40-36_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC1-BGKcLV40-36_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28470