EXOSC1 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV50-49	BGHcLV50-50
idx	1868	1869
TRCN#_or_BGC#	BGC#0001418	BGC#0001418
shRNA_or_gRNA_sequence	CCTGTGAGATACTGCATCCC	CCTGTGAGATACTGCATCCC
PAM	CGG	CGG
Name	EXOSC1_86	EXOSC1_86
Sample_ID	BGHcLV50-49	BGHcLV50-50
transduction_Date	7/29/25	7/29/25
days	D6	D6
RBP_name	EXOSC1	EXOSC1
qPCR_result	39.9	35.1
Ave_qPCR	37.5
RT-qPCR_primer-F	gagtggtggtagcccacagt
RT-qPCR_primer-R	tagggcactgcatctcacac
protein_conc	3883	3334
WB_result	73.2	70.3
Ave_WB
WB_DONE_date	8/19/25
MW	21kd
IP
antibody_Cat#	A303-885A	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	10057	10058

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV50-49	BGHcLV50-50
Sample_ID	BGHcLV50-49	BGHcLV50-50
Sample Name
Sample Name	EXOSC1-BGHcLV50-49	EXOSC1-BGHcLV50-50
RBP	EXOSC1	EXOSC1
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14456	14457

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV50-49	BGHcLV50-50
Sample #	9	10
Sample Name	EXOSC1-BGHcLV50-49	EXOSC1-BGHcLV50-50
Sample_Name_Alias
Index Well Position	A11	B11
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-10-01	2025-10-01
Lib_ID	Lib-251001	Lib-251001
Tecan_Location
Tecan
Tecan_date
Size_bp	287	293
Peak_Molarity	94.60	85.80
libSampleQC_DNA_Well	DNA_Library_set80/set1/A11.png	DNA_Library_set80/set1/B11.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set80/set1/A8.png	RNA_Library_set80/set1/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-10-03	2025-10-03
Sample_ID	BGHcLV50-49	BGHcLV50-50
RBP	EXOSC1	EXOSC1
Batch_ID	BGHcLV50	BGHcLV50
WB_result	73.200	70.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4824	4825

Sequencing Information

	BGHcLV50-49	BGHcLV50-50
Sample_ID	BGHcLV50-49	BGHcLV50-50
Sample Name	EXOSC1-BGHcLV50-49	EXOSC1-BGHcLV50-50
Pool ID	Pool-251003	Pool-251003
LocalServer_folder	set80	set80
total_reads	26,662,761	20,217,155
total_aligned_reads	23,772,396	17,456,584
unique_aligned_reads	22,456,230	16,536,912
percent_uniqueAligned	0.84223	0.81796
correlation_replicates	0.992384	0.992384
spikein_reads	62,366	64,844
percent_spikeins	0.00234	0.00321
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3479	3480

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-BGHcLV50-49_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3479	NovaSeq6000	100	paired-ended	1				NT-BGHcLV50-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32980
EXOSC1-BGHcLV50-49_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3479	NovaSeq6000	100	paired-ended	2				NT-BGHcLV50-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33004
EXOSC1-BGHcLV50-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3479					GRCh38	V40	EXOSC1-BGHcLV50-49_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC1-BGHcLV50-49_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33028
EXOSC1-BGHcLV50-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3479					GRCh38	V40	EXOSC1-BGHcLV50-49_Aligned.sortedByCoord.out.bam		ENCORE2	33052
EXOSC1-BGHcLV50-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3479					GRCh38	V40	EXOSC1-BGHcLV50-49_Aligned.sortedByCoord.out.bam		ENCORE2	33076
EXOSC1-BGHcLV50-49_Signal.Unique.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3479					GRCh38	V40	EXOSC1-BGHcLV50-49_Aligned.sortedByCoord.out.bam		ENCORE2	33100
EXOSC1-BGHcLV50-49_Signal.Unique.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3479					GRCh38	V40	EXOSC1-BGHcLV50-49_Aligned.sortedByCoord.out.bam		ENCORE2	33124
EXOSC1-BGHcLV50-49_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3479					GRCh38	V40	EXOSC1-BGHcLV50-49_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC1-BGHcLV50-49_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33148
EXOSC1-BGHcLV50-50_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3480	NovaSeq6000	100	paired-ended	1				NT-BGHcLV50-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32981
EXOSC1-BGHcLV50-50_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set80/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3480	NovaSeq6000	100	paired-ended	2				NT-BGHcLV50-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV50-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33005
EXOSC1-BGHcLV50-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3480					GRCh38	V40	EXOSC1-BGHcLV50-50_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC1-BGHcLV50-50_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33029
EXOSC1-BGHcLV50-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3480					GRCh38	V40	EXOSC1-BGHcLV50-50_Aligned.sortedByCoord.out.bam		ENCORE2	33053
EXOSC1-BGHcLV50-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3480					GRCh38	V40	EXOSC1-BGHcLV50-50_Aligned.sortedByCoord.out.bam		ENCORE2	33077
EXOSC1-BGHcLV50-50_Signal.Unique.strand-.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3480					GRCh38	V40	EXOSC1-BGHcLV50-50_Aligned.sortedByCoord.out.bam		ENCORE2	33101
EXOSC1-BGHcLV50-50_Signal.Unique.strand+.bw	ENCODE_DATA/set80/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3480					GRCh38	V40	EXOSC1-BGHcLV50-50_Aligned.sortedByCoord.out.bam		ENCORE2	33125
EXOSC1-BGHcLV50-50_quant.sf	ENCODE_DATA/set80/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3480					GRCh38	V40	EXOSC1-BGHcLV50-50_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,EXOSC1-BGHcLV50-50_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33149