SMG9 RNA-Seq in K562

General Information


RBP	SMG9
Cell_Line	K562
Method	CRISPR
Exp_Name	SMG9-BGKcLV33-K562
ENCODE_series_ID	ENCSR648SPD
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR971FJU
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SMG9-BGKcLV33-61
Rep2	SMG9-BGKcLV33-62
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	band isn't on the position
Rep2_WB
Antibody Cat#	A300-784A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	912

Experiment Information (Status: Released)

	BGKcLV33-57	BGKcLV33-57	BGKcLV33-58	BGKcLV33-58
idx	1159	1248	1160	1249
TRCN#_or_BGC#	BGC#0000876	BGC#0000872	BGC#0000876	BGC#0000872
shRNA_or_gRNA_sequence	ATGGGATAGAGCGGCGGCGA	GAAAATGCTAGTTACCGATT	ATGGGATAGAGCGGCGGCGA	GAAAATGCTAGTTACCGATT
PAM	CGG	TGG	CGG	TGG
Name	SMG9_91	SMG7_92	SMG9_91	SMG7_92
Sample_ID	BGKcLV33-57	BGKcLV33-57	BGKcLV33-58	BGKcLV33-58
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	SMG9	SMG7	SMG9	SMG7
qPCR_result		0.0		0.0
Ave_qPCR		0.0
RT-qPCR_primer-F		tgctgtgaagttccctttcc
RT-qPCR_primer-R		cagaaacaccccacttggtt
protein_conc	430	1847	424	1972
WB_result	77.8	66.9	71.8	76.2066009
Ave_WB	74.8	71.5
WB_DONE_date	2/1/22	3/16/22
MW	58kd	127kd
IP
antibody_Cat#	A302-210A	A302-170A	LOT #1	LOT #1
Antibody DCC ID		NO ID		8/4/22
submitted_to_DCC_date
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	5299	5390	5300	5391

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMG7	Product_ID: A302-170A Lot_ID: 1 Source: Bethyl Labs Target Name: SMG7-human

Experiment Status

	BGKcLV33-57	BGKcLV33-57	BGKcLV33-58	BGKcLV33-58
Sample_ID	BGKcLV33-57	BGKcLV33-57	BGKcLV33-58	BGKcLV33-58
Sample Name
Sample Name	SMG7-BGKcLV33-57		SMG7-BGKcLV33-58
RBP	SMG7	SMG9	SMG7	SMG9
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	10673	10743	10674	10744

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-57	BGKcLV33-58
Sample #	43	44
Sample Name	SMG7-BGKcLV33-57	SMG7-BGKcLV33-58
Sample_Name_Alias
Index Well Position	C06	D06
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	290	300
Peak_Molarity	74.60	59.00
libSampleQC_DNA_Well	DNA_Library_set53/set1/C10.png	DNA_Library_set53/set1/D10.png
RIN	9.7	10.0
libSample_RNA_Well	RNA_Library_set53/set1/C6.png	RNA_Library_set53/set1/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-57	BGKcLV33-58
RBP	SMG7	SMG7
Batch_ID	BGKcLV33	BGKcLV33
WB_result	66.900	76.207
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3304	3305

Sequencing Information

	BGKcLV33-57	BGKcLV33-58
Sample_ID	BGKcLV33-57	BGKcLV33-58
Sample Name	SMG7-BGKcLV33-57	SMG7-BGKcLV33-58
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	89,144,086	101,566,694
total_aligned_reads	81,667,922	94,258,874
unique_aligned_reads	75,168,872	86,421,602
percent_uniqueAligned	0.84323	0.85089
correlation_replicates	0.991358	0.991358
spikein_reads	8,360	5,268
percent_spikeins	0.00009	0.00005
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2071	2072

Data Submission Information

	BGKcLV33-57	BGKcLV33-57	BGKcLV33-57	BGKcLV33-57	BGKcLV33-57	BGKcLV33-57	BGKcLV33-58	BGKcLV33-58	BGKcLV33-58	BGKcLV33-58
ENCODE_alias	brenton-graveley:SMG7-BGKcLV33	brenton-graveley:SMG7-BGKcLV33-57	brenton-graveley:L-SMG7-BGKcLV33-57	brenton-graveley:SMG7-BGKcLV33-57_S97_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG7-BGKcLV33-57_S97_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG7-BGKcLV33-K562	brenton-graveley:SMG7-BGKcLV33-58	brenton-graveley:L-SMG7-BGKcLV33-58	brenton-graveley:SMG7-BGKcLV33-58_S98_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG7-BGKcLV33-58_S98_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR157IJG	ENCBS385NOB	ENCLB394CWU	ENCFF886DPB	ENCFF270QHG	ENCSR871SAO	ENCBS248EXP	ENCLB521CIG	ENCFF608VMS	ENCFF270BEV
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	BGKcLV33-57	BGKcLV33-57	BGKcLV33-57	BGKcLV33-57	BGKcLV33-57	BGKcLV33-57	BGKcLV33-58	BGKcLV33-58	BGKcLV33-58	BGKcLV33-58
Sample Name	SMG7-BGKcLV33-57	SMG7-BGKcLV33-57	SMG7-BGKcLV33-57	SMG7-BGKcLV33-57	SMG7-BGKcLV33-57	SMG7-BGKcLV33-57	SMG7-BGKcLV33-58	SMG7-BGKcLV33-58	SMG7-BGKcLV33-58	SMG7-BGKcLV33-58
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		SMG7-BGKcLV33-57.pdf	L-SMG7-BGKcLV33-57.pdf				SMG7-BGKcLV33-58.pdf	L-SMG7-BGKcLV33-58.pdf
ID	7491	7591	7701	7813	7923	7981	7592	7702	7814	7924

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
SMG7-BGKcLV33-57_S97_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2071	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	6651
SMG7-BGKcLV33-57_S97_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2071	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	6707
SMG7-BGKcLV33-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2071					GRCh38	V40	SMG7-BGKcLV33-57_S97_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG7-BGKcLV33-57_S97_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18128
SMG7-BGKcLV33-57_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	2071					GRCh38	V40	SMG7-BGKcLV33-57/Aligned.sortedByCoord.out.bam		ENCORE2	18184
SMG7-BGKcLV33-57_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	2071					GRCh38	V40	SMG7-BGKcLV33-57/Aligned.sortedByCoord.out.bam		ENCORE2	18240
SMG7-BGKcLV33-57_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	2071					GRCh38	V40	SMG7-BGKcLV33-57/Aligned.sortedByCoord.out.bam		ENCORE2	18296
SMG7-BGKcLV33-57_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	2071					GRCh38	V40	SMG7-BGKcLV33-57/Aligned.sortedByCoord.out.bam		ENCORE2	18352
SMG7-BGKcLV33-57_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2071					GRCh38	V40	SMG7-BGKcLV33-57_S97_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG7-BGKcLV33-57_S97_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18408
SMG7-BGKcLV33-58_S98_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2072	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	6652
SMG7-BGKcLV33-58_S98_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2072	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	6708
SMG7-BGKcLV33-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2072					GRCh38	V40	SMG7-BGKcLV33-58_S98_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG7-BGKcLV33-58_S98_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18129
SMG7-BGKcLV33-58_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	2072					GRCh38	V40	SMG7-BGKcLV33-58/Aligned.sortedByCoord.out.bam		ENCORE2	18185
SMG7-BGKcLV33-58_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	2072					GRCh38	V40	SMG7-BGKcLV33-58/Aligned.sortedByCoord.out.bam		ENCORE2	18241
SMG7-BGKcLV33-58_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	2072					GRCh38	V40	SMG7-BGKcLV33-58/Aligned.sortedByCoord.out.bam		ENCORE2	18297
SMG7-BGKcLV33-58_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	2072					GRCh38	V40	SMG7-BGKcLV33-58/Aligned.sortedByCoord.out.bam		ENCORE2	18353
SMG7-BGKcLV33-58_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2072					GRCh38	V40	SMG7-BGKcLV33-58_S98_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG7-BGKcLV33-58_S98_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18409