SMG8 RNA-Seq in K562

General Information


RBP	SMG8
Cell_Line	K562
Method	CRISPR
Exp_Name	SMG8-BGKcLV33-K562
ENCODE_series_ID	ENCSR793HOO
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR869YRR
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SMG8-BGKcLV33-59
Rep2	SMG8-BGKcLV33-60
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	band isn't on the position
Rep2_WB
Antibody Cat#	A305-567A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	911

Experiment Information (Status: Released)

	BGKcLV33-55	BGKcLV33-55	BGKcLV33-56	BGKcLV33-56
idx	1157	1246	1158	1247
TRCN#_or_BGC#	BGC#0000873	BGC#0000870	BGC#0000873	BGC#0000870
shRNA_or_gRNA_sequence	CGCGGAAGGTAACCGAACTG	ATGTGCCTACAGGACGCACC	CGCGGAAGGTAACCGAACTG	ATGTGCCTACAGGACGCACC
PAM	AGG	TGG	AGG	TGG
Name	SMG8_97	SMG5_92	SMG8_97	SMG5_92
Sample_ID	BGKcLV33-55	BGKcLV33-55	BGKcLV33-56	BGKcLV33-56
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	SMG8	SMG5	SMG8	SMG5
qPCR_result		68.6718798		54.8
Ave_qPCR		61.7
RT-qPCR_primer-F		tatgggagaaaggctgagga
RT-qPCR_primer-R		aagccaataccagcaaccag
protein_conc	421	2218	588	2695
WB_result	no band on the position	64.1		66.1
Ave_WB		65.1
WB_DONE_date	2/1/22	3/10/22
MW	110kd	114kd
IP
antibody_Cat#	A301-471A	A302-804A	LOT #1	LOT #1
Antibody DCC ID		ENCAB166GHC		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	5297	5388	5298	5389

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SMG5	Product_ID: A302-804A Lot_ID: 1 Source: Bethyl Labs Target Name: SMG5-human

Experiment Status

	BGKcLV33-55	BGKcLV33-55	BGKcLV33-56	BGKcLV33-56
Sample_ID	BGKcLV33-55	BGKcLV33-55	BGKcLV33-56	BGKcLV33-56
Sample Name
Sample Name	SMG5-BGKcLV33-55		SMG5-BGKcLV33-56
RBP	SMG5	SMG8	SMG5	SMG8
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	10671	10741	10672	10742

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-55	BGKcLV33-56
Sample #	41	42
Sample Name	SMG5-BGKcLV33-55	SMG5-BGKcLV33-56
Sample_Name_Alias
Index Well Position	A06	B06
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	292	302
Peak_Molarity	56.30	55.40
libSampleQC_DNA_Well	DNA_Library_set53/set1/A10.png	DNA_Library_set53/set1/B10.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set53/set1/A6.png	RNA_Library_set53/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-55	BGKcLV33-56
RBP	SMG5	SMG5
Batch_ID	BGKcLV33	BGKcLV33
WB_result	64.100	66.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3302	3303

Sequencing Information

	BGKcLV33-55	BGKcLV33-56
Sample_ID	BGKcLV33-55	BGKcLV33-56
Sample Name	SMG5-BGKcLV33-55	SMG5-BGKcLV33-56
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	102,263,124	81,369,490
total_aligned_reads	94,270,052	74,416,034
unique_aligned_reads	86,320,992	67,762,684
percent_uniqueAligned	0.84411	0.83278
correlation_replicates	0.993921	0.993921
spikein_reads	18,104	9,756
percent_spikeins	0.00018	0.00012
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2069	2070

Data Submission Information

	BGKcLV33-55	BGKcLV33-55	BGKcLV33-55	BGKcLV33-55	BGKcLV33-55	BGKcLV33-55	BGKcLV33-56	BGKcLV33-56	BGKcLV33-56	BGKcLV33-56
ENCODE_alias	brenton-graveley:SMG5-BGKcLV33	brenton-graveley:SMG5-BGKcLV33-55	brenton-graveley:L-SMG5-BGKcLV33-55	brenton-graveley:SMG5-BGKcLV33-55_S95_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG5-BGKcLV33-55_S95_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG5-BGKcLV33-K562	brenton-graveley:SMG5-BGKcLV33-56	brenton-graveley:L-SMG5-BGKcLV33-56	brenton-graveley:SMG5-BGKcLV33-56_S96_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SMG5-BGKcLV33-56_S96_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR183WOW	ENCBS085BKT	ENCLB473BZI	ENCFF089ZVL	ENCFF162LMP	ENCSR801MKG	ENCBS568KMK	ENCLB846SVD	ENCFF122SRO	ENCFF038ATC
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	BGKcLV33-55	BGKcLV33-55	BGKcLV33-55	BGKcLV33-55	BGKcLV33-55	BGKcLV33-55	BGKcLV33-56	BGKcLV33-56	BGKcLV33-56	BGKcLV33-56
Sample Name	SMG5-BGKcLV33-55	SMG5-BGKcLV33-55	SMG5-BGKcLV33-55	SMG5-BGKcLV33-55	SMG5-BGKcLV33-55	SMG5-BGKcLV33-55	SMG5-BGKcLV33-56	SMG5-BGKcLV33-56	SMG5-BGKcLV33-56	SMG5-BGKcLV33-56
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		SMG5-BGKcLV33-55.pdf	L-SMG5-BGKcLV33-55.pdf				SMG5-BGKcLV33-56.pdf	L-SMG5-BGKcLV33-56.pdf
ID	7490	7589	7699	7811	7921	7980	7590	7700	7812	7922

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
SMG5-BGKcLV33-55_S95_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2069	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	6649
SMG5-BGKcLV33-55_S95_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2069	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	6705
SMG5-BGKcLV33-55_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2069					GRCh38	V40	SMG5-BGKcLV33-55_S95_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG5-BGKcLV33-55_S95_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18126
SMG5-BGKcLV33-55_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	2069					GRCh38	V40	SMG5-BGKcLV33-55/Aligned.sortedByCoord.out.bam		ENCORE2	18182
SMG5-BGKcLV33-55_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	2069					GRCh38	V40	SMG5-BGKcLV33-55/Aligned.sortedByCoord.out.bam		ENCORE2	18238
SMG5-BGKcLV33-55_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	2069					GRCh38	V40	SMG5-BGKcLV33-55/Aligned.sortedByCoord.out.bam		ENCORE2	18294
SMG5-BGKcLV33-55_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	2069					GRCh38	V40	SMG5-BGKcLV33-55/Aligned.sortedByCoord.out.bam		ENCORE2	18350
SMG5-BGKcLV33-55_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2069					GRCh38	V40	SMG5-BGKcLV33-55_S95_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG5-BGKcLV33-55_S95_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18406
SMG5-BGKcLV33-56_S96_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2070	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	6650
SMG5-BGKcLV33-56_S96_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2070	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	6706
SMG5-BGKcLV33-56_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2070					GRCh38	V40	SMG5-BGKcLV33-56_S96_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG5-BGKcLV33-56_S96_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18127
SMG5-BGKcLV33-56_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	2070					GRCh38	V40	SMG5-BGKcLV33-56/Aligned.sortedByCoord.out.bam		ENCORE2	18183
SMG5-BGKcLV33-56_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	2070					GRCh38	V40	SMG5-BGKcLV33-56/Aligned.sortedByCoord.out.bam		ENCORE2	18239
SMG5-BGKcLV33-56_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	2070					GRCh38	V40	SMG5-BGKcLV33-56/Aligned.sortedByCoord.out.bam		ENCORE2	18295
SMG5-BGKcLV33-56_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	2070					GRCh38	V40	SMG5-BGKcLV33-56/Aligned.sortedByCoord.out.bam		ENCORE2	18351
SMG5-BGKcLV33-56_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2070					GRCh38	V40	SMG5-BGKcLV33-56_S96_L002_R1_001.filtered.trimmed.paired.fastq.gz,SMG5-BGKcLV33-56_S96_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18407