SMG8 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV49-99	BGHcLV49-100
idx	1802	1803
TRCN#_or_BGC#	BGC#0000873	BGC#0000873
shRNA_or_gRNA_sequence	CGCGGAAGGTAACCGAACTG	CGCGGAAGGTAACCGAACTG
PAM	AGG	AGG
Name	SMG8_97	SMG8_97
Sample_ID	BGHcLV49-99	BGHcLV49-100
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	SMG8	SMG8
qPCR_result	21.9	11.6
Ave_qPCR	16.7
RT-qPCR_primer-F	tgttgtggttcctgatgctc
RT-qPCR_primer-R	tcaggtggaagggtgatttc
protein_conc	5107	4302
WB_result	59.3	77.1
Ave_WB
WB_DONE_date	7/10/25
MW	110kd
IP
antibody_Cat#	A301-471A	LOT #1
Antibody DCC ID	ENCAB236BQW
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9991	9992

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMG8	Product_ID: A301-471A Lot_ID: 1 Source: Bethyl Labs Target Name: SMG8-human

Experiment Status

	BGHcLV49-99	BGHcLV49-100
Sample_ID	BGHcLV49-99	BGHcLV49-100
Sample Name
Sample Name	SMG8-BGHcLV49-99	SMG8-BGHcLV49-100
RBP	SMG8	SMG8
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2
Note
ID	14364	14365

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-99	BGHcLV49-100
Sample #	61	62
Sample Name	SMG8-BGHcLV49-99	SMG8-BGHcLV49-100
Sample_Name_Alias
Index Well Position	G08	H08
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	264	251
Peak_Molarity	68.00	52.50
libSampleQC_DNA_Well	DNA_Library_set81/set1/H5.png	DNA_Library_set81/set1/G5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set81/set1/H8.png	RNA_Library_set81/set1/G8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-10
Sample_ID	BGHcLV49-99	BGHcLV49-100
RBP	SMG8	SMG8
Batch_ID	BGHcLV49	BGHcLV49
WB_result	59.300	77.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4806	4807

Sequencing Information

	BGHcLV49-99	BGHcLV49-100
Sample_ID	BGHcLV49-99	BGHcLV49-100
Sample Name	SMG8-BGHcLV49-99	SMG8-BGHcLV49-100
Pool ID	Pool-250916	Pool-250916
LocalServer_folder	set81	set81
total_reads	68,238,691	59,602,864
total_aligned_reads	59,782,966	49,753,835
unique_aligned_reads	56,215,787	46,830,115
percent_uniqueAligned	0.82381	0.78570
correlation_replicates	0.999160	0.999160
spikein_reads	155,920	190,822
percent_spikeins	0.00228	0.00320
original_ReadLength	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3531	3532

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
SMG8-BGHcLV49-99_S149_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3531	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	33207
SMG8-BGHcLV49-99_S149_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3531	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	33253
SMG8-BGHcLV49-99_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3531					GRCh38	V40	SMG8-BGHcLV49-99_S149_L008_R1_001.filtered.trimmed.paired.fastq.gz,SMG8-BGHcLV49-99_S149_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33299
SMG8-BGHcLV49-99_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	3531					GRCh38	V40	SMG8-BGHcLV49-99_Aligned.sortedByCoord.out.bam		ENCORE2	33345
SMG8-BGHcLV49-99_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	3531					GRCh38	V40	SMG8-BGHcLV49-99_Aligned.sortedByCoord.out.bam		ENCORE2	33391
SMG8-BGHcLV49-99_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	3531					GRCh38	V40	SMG8-BGHcLV49-99_Aligned.sortedByCoord.out.bam		ENCORE2	33437
SMG8-BGHcLV49-99_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	3531					GRCh38	V40	SMG8-BGHcLV49-99_Aligned.sortedByCoord.out.bam		ENCORE2	33483
SMG8-BGHcLV49-99_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3531					GRCh38	V40	SMG8-BGHcLV49-99_S149_L008_R1_001.filtered.trimmed.paired.fastq.gz,SMG8-BGHcLV49-99_S149_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33529
SMG8-BGHcLV49-100_S146_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3532	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	33206
SMG8-BGHcLV49-100_S146_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3532	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	33252
SMG8-BGHcLV49-100_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3532					GRCh38	V40	SMG8-BGHcLV49-100_S146_L008_R1_001.filtered.trimmed.paired.fastq.gz,SMG8-BGHcLV49-100_S146_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33298
SMG8-BGHcLV49-100_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	3532					GRCh38	V40	SMG8-BGHcLV49-100_Aligned.sortedByCoord.out.bam		ENCORE2	33344
SMG8-BGHcLV49-100_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	3532					GRCh38	V40	SMG8-BGHcLV49-100_Aligned.sortedByCoord.out.bam		ENCORE2	33390
SMG8-BGHcLV49-100_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	3532					GRCh38	V40	SMG8-BGHcLV49-100_Aligned.sortedByCoord.out.bam		ENCORE2	33436
SMG8-BGHcLV49-100_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	3532					GRCh38	V40	SMG8-BGHcLV49-100_Aligned.sortedByCoord.out.bam		ENCORE2	33482
SMG8-BGHcLV49-100_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3532					GRCh38	V40	SMG8-BGHcLV49-100_S146_L008_R1_001.filtered.trimmed.paired.fastq.gz,SMG8-BGHcLV49-100_S146_L008_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	33528