SNUPN RNA-Seq in K562

Experiment Information (Status: Released)

	BGKcLV33-59	BGKcLV33-59	BGKcLV33-60	BGKcLV33-60
idx	1161	1250	1162	1251
TRCN#_or_BGC#	BGC#0000877	BGC#0000873	BGC#0000877	BGC#0000873
shRNA_or_gRNA_sequence	GCAGTTCCAGTAACCTCCGG	CGCGGAAGGTAACCGAACTG	GCAGTTCCAGTAACCTCCGG	CGCGGAAGGTAACCGAACTG
PAM	CGG	AGG	CGG	AGG
Name	SNUPN_92	SMG8_97	SNUPN_92	SMG8_97
Sample_ID	BGKcLV33-59	BGKcLV33-59	BGKcLV33-60	BGKcLV33-60
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	SNUPN	SMG8	SNUPN	SMG8
qPCR_result		0.0		0.0
Ave_qPCR		0.0
RT-qPCR_primer-F		tgttgtggttcctgatgctc
RT-qPCR_primer-R		tcaggtggaagggtgatttc
protein_conc	488	2284	540	2127
WB_result	band isn't on the position	83.0		84.7
Ave_WB		83.9
WB_DONE_date	2/1/22	3/10/22,3/11/22
MW	41kd	110kd
IP
antibody_Cat#	A305-567A	A301-471A	LOT #1	LOT #1
Antibody DCC ID		ENCAB236BQW		8/4/22
submitted_to_DCC_date		8/16/22
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action		Ready		Ready
Library_start_date		04/13/22		04/13/22
repeat_library
Note
ID	5301	5392	5302	5393

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

	BGKcLV33-59	BGKcLV33-59	BGKcLV33-60	BGKcLV33-60
Sample_ID	BGKcLV33-59	BGKcLV33-59	BGKcLV33-60	BGKcLV33-60
Sample Name
Sample Name	SMG8-BGKcLV33-59		SMG8-BGKcLV33-60
RBP	SMG8	SNUPN	SMG8	SNUPN
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2022-10-28	2022-03-30	2022-10-28	2022-03-30
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	10675	10745	10676	10746

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-59	BGKcLV33-60
Sample #	45	46
Sample Name	SMG8-BGKcLV33-59	SMG8-BGKcLV33-60
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-04-06	2022-04-06
Lib_ID	Lib-220406	Lib-220406
Tecan_Location
Tecan
Tecan_date
Size_bp	313	311
Peak_Molarity	57.10	51.50
libSampleQC_DNA_Well	DNA_Library_set53/set1/E10.png	DNA_Library_set53/set1/F10.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set53/set1/E6.png	RNA_Library_set53/set1/F6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-59	BGKcLV33-60
RBP	SMG8	SMG8
Batch_ID	BGKcLV33	BGKcLV33
WB_result	83.000	84.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3306	3307

Sequencing Information

	BGKcLV33-59	BGKcLV33-60
Sample_ID	BGKcLV33-59	BGKcLV33-60
Sample Name	SMG8-BGKcLV33-59	SMG8-BGKcLV33-60
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	109,406,658	84,459,618
total_aligned_reads	101,706,262	77,962,834
unique_aligned_reads	92,680,394	71,064,900
percent_uniqueAligned	0.84712	0.84141
correlation_replicates	0.997936	0.997936
spikein_reads	9,176	2,732
percent_spikeins	0.00008	0.00003
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2073	2074

Data Submission Information

	BGKcLV33-59	BGKcLV33-59	BGKcLV33-59	BGKcLV33-59	BGKcLV33-59	BGKcLV33-59	BGKcLV33-60	BGKcLV33-60	BGKcLV33-60	BGKcLV33-60
ENCODE_alias	brenton-graveley:SMG8-BGKcLV33	brenton-graveley:SMG8-BGKcLV33-59	brenton-graveley:L-SMG8-BGKcLV33-59	brenton-graveley:SMG8-BGKcLV33-59_S99_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG8-BGKcLV33-59_S99_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG8-BGKcLV33-K562	brenton-graveley:SMG8-BGKcLV33-60	brenton-graveley:L-SMG8-BGKcLV33-60	brenton-graveley:SMG8-BGKcLV33-60_S100_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG8-BGKcLV33-60_S100_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR869YRR	ENCBS287UQB	ENCLB278DCO	ENCFF527QSW	ENCFF695TLS	ENCSR793HOO	ENCBS572GTT	ENCLB997NCI	ENCFF283WHC	ENCFF397IVI
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV33-59	BGKcLV33-59	BGKcLV33-59	BGKcLV33-59	BGKcLV33-59	BGKcLV33-59	BGKcLV33-60	BGKcLV33-60	BGKcLV33-60	BGKcLV33-60
Sample Name	SMG8-BGKcLV33-59	SMG8-BGKcLV33-59	SMG8-BGKcLV33-59	SMG8-BGKcLV33-59	SMG8-BGKcLV33-59	SMG8-BGKcLV33-59	SMG8-BGKcLV33-60	SMG8-BGKcLV33-60	SMG8-BGKcLV33-60	SMG8-BGKcLV33-60
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV53_biosample_protocol	LV53_library_protocol				LV53_biosample_protocol	LV53_library_protocol
protocol_URL		SMG8-BGKcLV33-59.pdf	L-SMG8-BGKcLV33-59.pdf				SMG8-BGKcLV33-60.pdf	L-SMG8-BGKcLV33-60.pdf
ID	7492	7593	7703	7815	7925	7982	7594	7704	7816	7926

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-BGKcLV33-59_S99_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2073	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6653
SMG8-BGKcLV33-59_S99_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2073	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6709
SMG8-BGKcLV33-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2073					GRCh38	V40	SMG8-BGKcLV33-59_S99_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG8-BGKcLV33-59_S99_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18130
SMG8-BGKcLV33-59_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2073					GRCh38	V40	SMG8-BGKcLV33-59/Aligned.sortedByCoord.out.bam		ENCORE2	18186
SMG8-BGKcLV33-59_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2073					GRCh38	V40	SMG8-BGKcLV33-59/Aligned.sortedByCoord.out.bam		ENCORE2	18242
SMG8-BGKcLV33-59_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2073					GRCh38	V40	SMG8-BGKcLV33-59/Aligned.sortedByCoord.out.bam		ENCORE2	18298
SMG8-BGKcLV33-59_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2073					GRCh38	V40	SMG8-BGKcLV33-59/Aligned.sortedByCoord.out.bam		ENCORE2	18354
SMG8-BGKcLV33-59_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2073					GRCh38	V40	SMG8-BGKcLV33-59_S99_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG8-BGKcLV33-59_S99_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18410
SMG8-BGKcLV33-60_S100_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2074	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6654
SMG8-BGKcLV33-60_S100_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2074	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6710
SMG8-BGKcLV33-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2074					GRCh38	V40	SMG8-BGKcLV33-60_S100_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG8-BGKcLV33-60_S100_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18131
SMG8-BGKcLV33-60_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2074					GRCh38	V40	SMG8-BGKcLV33-60/Aligned.sortedByCoord.out.bam		ENCORE2	18187
SMG8-BGKcLV33-60_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2074					GRCh38	V40	SMG8-BGKcLV33-60/Aligned.sortedByCoord.out.bam		ENCORE2	18243
SMG8-BGKcLV33-60_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2074					GRCh38	V40	SMG8-BGKcLV33-60/Aligned.sortedByCoord.out.bam		ENCORE2	18299
SMG8-BGKcLV33-60_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2074					GRCh38	V40	SMG8-BGKcLV33-60/Aligned.sortedByCoord.out.bam		ENCORE2	18355
SMG8-BGKcLV33-60_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2074					GRCh38	V40	SMG8-BGKcLV33-60_S100_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG8-BGKcLV33-60_S100_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18411