SMG9 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-101	BGHcLV49-101	BGHcLV49-102	BGHcLV49-102
idx	1804	1806	1805	1807
TRCN#_or_BGC#	BGC#0000876	BGC#0000876	BGC#0000876	BGC#0000876
shRNA_or_gRNA_sequence	ATGGGATAGAGCGGCGGCGA	ATGGGATAGAGCGGCGGCGA	ATGGGATAGAGCGGCGGCGA	ATGGGATAGAGCGGCGGCGA
PAM	CGG	CGG	CGG	CGG
Name	SMG9_91	SMG9_91	SMG9_91	SMG9_91
Sample_ID	BGHcLV49-101	BGHcLV49-101	BGHcLV49-102	BGHcLV49-102
transduction_Date	6/6/25	6/6/25	6/6/25	6/6/25
days	D6	D6	D6	D6
RBP_name	SMG9	SMG9	SMG9	SMG9
qPCR_result	17.0		0.0
Ave_qPCR	8.5
RT-qPCR_primer-F	ttggtggatgaccagatgaa
RT-qPCR_primer-R	atgaccatggacttgcctgt
protein_conc	4694	4694	5099	5099
WB_result	94.5		83.3
Ave_WB
WB_DONE_date	7/3/25	7/21/25		no band on the posio
MW	58kd	58kd
IP
antibody_Cat#	A302-210A	A302-211A	LOT #1	LOT #1
Antibody DCC ID	ENCAB220KQW
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	9993	9995	9994	9996

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMG9	Product_ID: A302-210A Lot_ID: 1 Source: Bethyl Labs Target Name: SMG9-human

Experiment Status

	BGHcLV49-101	BGHcLV49-101	BGHcLV49-102	BGHcLV49-102
Sample_ID	BGHcLV49-101	BGHcLV49-101	BGHcLV49-102	BGHcLV49-102
Sample Name
Sample Name	SMG9-BGHcLV49-101		SMG9-BGHcLV49-102
RBP	SMG9	SMG9	SMG9	SMG9
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Sequenced	NotSatisfied	Sequenced	NotSatisfied
Status_date	2025-10-30	2025-08-12	2025-10-30	2025-08-12
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14366	14436	14367	14437

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-101	BGHcLV49-102
Sample #	63	64
Sample Name	SMG9-BGHcLV49-101	SMG9-BGHcLV49-102
Sample_Name_Alias
Index Well Position	A09	B09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-20	2025-08-20
Lib_ID	Lib-250820	Lib-250820
Tecan_Location
Tecan
Tecan_date
Size_bp	269	262
Peak_Molarity	68.50	79.70
libSampleQC_DNA_Well	DNA_Library_set81/set1/A6.png	DNA_Library_set81/set1/B6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set81/set1/A9.png	RNA_Library_set81/set1/B9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-101	BGHcLV49-102
RBP	SMG9	SMG9
Batch_ID	BGHcLV49	BGHcLV49
WB_result	94.500	83.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4808	4809

Sequencing Information

	BGHcLV49-101	BGHcLV49-102
Sample_ID	BGHcLV49-101	BGHcLV49-102
Sample Name	SMG9-BGHcLV49-101	SMG9-BGHcLV49-102
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	42,985,141	29,579,247
total_aligned_reads	37,274,345	25,394,339
unique_aligned_reads	35,070,704	23,914,115
percent_uniqueAligned	0.81588	0.80848
correlation_replicates	0.999288	0.999288
spikein_reads	139,624	78,852
percent_spikeins	0.00325	0.00267
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3533	3534

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
SMG9-BGHcLV49-101_S128_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3533	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33208
SMG9-BGHcLV49-101_S128_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3533	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33254
SMG9-BGHcLV49-101_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3533					GRCh38	V40	SMG9-BGHcLV49-101_S128_L008_R1_001.filtered.trimmed.paired.fastq.gz,SMG9-BGHcLV49-101_S128_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33300
SMG9-BGHcLV49-101_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3533					GRCh38	V40	SMG9-BGHcLV49-101_Aligned.sortedByCoord.out.bam		ENCORE2	33346
SMG9-BGHcLV49-101_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3533					GRCh38	V40	SMG9-BGHcLV49-101_Aligned.sortedByCoord.out.bam		ENCORE2	33392
SMG9-BGHcLV49-101_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3533					GRCh38	V40	SMG9-BGHcLV49-101_Aligned.sortedByCoord.out.bam		ENCORE2	33438
SMG9-BGHcLV49-101_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3533					GRCh38	V40	SMG9-BGHcLV49-101_Aligned.sortedByCoord.out.bam		ENCORE2	33484
SMG9-BGHcLV49-101_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3533					GRCh38	V40	SMG9-BGHcLV49-101_S128_L008_R1_001.filtered.trimmed.paired.fastq.gz,SMG9-BGHcLV49-101_S128_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33530
SMG9-BGHcLV49-102_S154_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3534	NovaSeq6000	100	paired-ended	1				NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33209
SMG9-BGHcLV49-102_S154_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3534	NovaSeq6000	100	paired-ended	2				NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33255
SMG9-BGHcLV49-102_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3534					GRCh38	V40	SMG9-BGHcLV49-102_S154_L008_R1_001.filtered.trimmed.paired.fastq.gz,SMG9-BGHcLV49-102_S154_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33301
SMG9-BGHcLV49-102_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3534					GRCh38	V40	SMG9-BGHcLV49-102_Aligned.sortedByCoord.out.bam		ENCORE2	33347
SMG9-BGHcLV49-102_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3534					GRCh38	V40	SMG9-BGHcLV49-102_Aligned.sortedByCoord.out.bam		ENCORE2	33393
SMG9-BGHcLV49-102_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3534					GRCh38	V40	SMG9-BGHcLV49-102_Aligned.sortedByCoord.out.bam		ENCORE2	33439
SMG9-BGHcLV49-102_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3534					GRCh38	V40	SMG9-BGHcLV49-102_Aligned.sortedByCoord.out.bam		ENCORE2	33485
SMG9-BGHcLV49-102_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3534					GRCh38	V40	SMG9-BGHcLV49-102_S154_L008_R1_001.filtered.trimmed.paired.fastq.gz,SMG9-BGHcLV49-102_S154_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33531