SMG5 RNA-Seq in K562

General Information


RBP	SMG5
Cell_Line	K562
Method	CRISPR
Exp_Name	SMG5-BGKcLV33-K562
ENCODE_series_ID	ENCSR801MKG
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR183WOW
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SMG5-BGKcLV33-55
Rep2	SMG5-BGKcLV33-56
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	no band on the position
Rep2_WB
Antibody Cat#	A301-471A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	909

Experiment Information (Status: Released)

	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-52	BGKcLV33-52	BGKcLV33-52
idx	1153	1240	1242	1154	1241	1243
TRCN#_or_BGC#	BGC#0000869	BGC#0000863	BGC#0000863	BGC#0000869	BGC#0000863	BGC#0000863
shRNA_or_gRNA_sequence	ACCGGTAAAGCCGCTTAGTG	TGGCATCGTGCTGAATCGGC	TGGCATCGTGCTGAATCGGC	ACCGGTAAAGCCGCTTAGTG	TGGCATCGTGCTGAATCGGC	TGGCATCGTGCTGAATCGGC
PAM	TGG	CGG	CGG	TGG	CGG	CGG
Name	SMG5_96	SF3B2_94	SF3B2_94	SMG5_96	SF3B2_94	SF3B2_94
Sample_ID	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-52	BGKcLV33-52	BGKcLV33-52
transduction_Date	12/7/21	2/22/22	2/22/22	12/7/21	2/22/22	2/22/22
days	D6	D6	D6	D6	D6	D6
RBP_name	SMG5	SF3B2	SF3B2	SMG5	SF3B2	SF3B2
qPCR_result		7.31437173	7.3		17.2230882	17.2
Ave_qPCR		12.3	12.3
RT-qPCR_primer-F		tgaaggagaagaagccagga	tgaaggagaagaagccagga
RT-qPCR_primer-R		ttcaggttgggatacgatgg	ttcaggttgggatacgatgg
protein_conc	267	1863	1863	521	2095	2095
WB_result	no band on the position	60.9	66.1		54.9	72.2
Ave_WB		57.9	69.2
WB_DONE_date	2/1/22	3/7/22	3/22/22
MW	114kd	100kd	100kd
IP
antibody_Cat#	A302-804A	A301-605A	A301-606A	LOT #1	LOT #1	LOT #1
Antibody DCC ID		ENCAB244MZF	ENCAB840ZAV		8/4/22	8/4/22
submitted_to_DCC_date		8/16/22
Rep1_TPM	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0
Action		Ready			Ready
Library_start_date		04/13/22			04/13/22
repeat_library
Note
ID	5293	5382	5384	5294	5383	5385

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SF3B2	Product_ID: A301-605A Lot_ID: 1 Source: Bethyl Labs Target Name: SF3B2-human
SF3B2	Product_ID: A301-606A Lot_ID: 1 Source: Bethyl Labs Target Name: SF3B2-human

Experiment Status

	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-52	BGKcLV33-52	BGKcLV33-52
Sample_ID	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-52	BGKcLV33-52	BGKcLV33-52
Sample Name
Sample Name	SF3B2-BGKcLV33-51			SF3B2-BGKcLV33-52
RBP	SF3B2	SMG5	SF3B2	SF3B2	SMG5	SF3B2
Cell_Line	K562	K562	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	NotSatisfied	Released	NotSatisfied	NotSatisfied
Status_date	2022-10-28	2022-03-30	2022-03-30	2022-10-28	2022-03-30	2022-03-30
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	10667	10737	10785	10668	10738	10786

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-51	BGKcLV33-52
Sample #	37	38
Sample Name	SF3B2-BGKcLV33-51	SF3B2-BGKcLV33-52
Sample_Name_Alias
Index Well Position	E05	F05
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	295
Peak_Molarity	60.60	49.80
libSampleQC_DNA_Well	DNA_Library_set53/set1/E9.png	DNA_Library_set53/set1/F9.png
RIN	9.6	9.8
libSample_RNA_Well	RNA_Library_set53/set1/E5.png	RNA_Library_set53/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-51	BGKcLV33-52
RBP	SF3B2	SF3B2
Batch_ID	BGKcLV33	BGKcLV33
WB_result	60.900	54.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3298	3299

Sequencing Information

	BGKcLV33-51	BGKcLV33-52
Sample_ID	BGKcLV33-51	BGKcLV33-52
Sample Name	SF3B2-BGKcLV33-51	SF3B2-BGKcLV33-52
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	155,957,652	144,130,422
total_aligned_reads	143,257,362	130,414,036
unique_aligned_reads	131,137,800	119,460,802
percent_uniqueAligned	0.84086	0.82884
correlation_replicates	0.998689	0.998689
spikein_reads	5,626	4,582
percent_spikeins	0.00004	0.00003
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2065	2066

Data Submission Information

	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-52	BGKcLV33-52	BGKcLV33-52	BGKcLV33-52
ENCODE_alias	brenton-graveley:SF3B2-BGKcLV33	brenton-graveley:SF3B2-BGKcLV33-51	brenton-graveley:L-SF3B2-BGKcLV33-51	brenton-graveley:SF3B2-BGKcLV33-51_S91_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3B2-BGKcLV33-51_S91_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3B2-BGKcLV33-K562	brenton-graveley:SF3B2-BGKcLV33-52	brenton-graveley:L-SF3B2-BGKcLV33-52	brenton-graveley:SF3B2-BGKcLV33-52_S92_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3B2-BGKcLV33-52_S92_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR447ARO	ENCBS533HEV	ENCLB417IOK	ENCFF869SCI	ENCFF384QWS	ENCSR292ATE	ENCBS793LRT	ENCLB461LRD	ENCFF651VSI	ENCFF536QXI
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	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-51	BGKcLV33-52	BGKcLV33-52	BGKcLV33-52	BGKcLV33-52
Sample Name	SF3B2-BGKcLV33-51	SF3B2-BGKcLV33-51	SF3B2-BGKcLV33-51	SF3B2-BGKcLV33-51	SF3B2-BGKcLV33-51	SF3B2-BGKcLV33-51	SF3B2-BGKcLV33-52	SF3B2-BGKcLV33-52	SF3B2-BGKcLV33-52	SF3B2-BGKcLV33-52
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		SF3B2-BGKcLV33-51.pdf	L-SF3B2-BGKcLV33-51.pdf				SF3B2-BGKcLV33-52.pdf	L-SF3B2-BGKcLV33-52.pdf
ID	7488	7585	7695	7807	7917	7978	7586	7696	7808	7918

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
SF3B2-BGKcLV33-51_S91_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2065	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	6643
SF3B2-BGKcLV33-51_S91_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2065	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	6699
SF3B2-BGKcLV33-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2065					GRCh38	V40	SF3B2-BGKcLV33-51_S91_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B2-BGKcLV33-51_S91_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18120
SF3B2-BGKcLV33-51_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	2065					GRCh38	V40	SF3B2-BGKcLV33-51/Aligned.sortedByCoord.out.bam		ENCORE2	18176
SF3B2-BGKcLV33-51_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	2065					GRCh38	V40	SF3B2-BGKcLV33-51/Aligned.sortedByCoord.out.bam		ENCORE2	18232
SF3B2-BGKcLV33-51_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	2065					GRCh38	V40	SF3B2-BGKcLV33-51/Aligned.sortedByCoord.out.bam		ENCORE2	18288
SF3B2-BGKcLV33-51_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	2065					GRCh38	V40	SF3B2-BGKcLV33-51/Aligned.sortedByCoord.out.bam		ENCORE2	18344
SF3B2-BGKcLV33-51_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2065					GRCh38	V40	SF3B2-BGKcLV33-51_S91_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B2-BGKcLV33-51_S91_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18400
SF3B2-BGKcLV33-52_S92_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2066	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	6644
SF3B2-BGKcLV33-52_S92_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2066	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	6700
SF3B2-BGKcLV33-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2066					GRCh38	V40	SF3B2-BGKcLV33-52_S92_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B2-BGKcLV33-52_S92_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18121
SF3B2-BGKcLV33-52_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	2066					GRCh38	V40	SF3B2-BGKcLV33-52/Aligned.sortedByCoord.out.bam		ENCORE2	18177
SF3B2-BGKcLV33-52_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	2066					GRCh38	V40	SF3B2-BGKcLV33-52/Aligned.sortedByCoord.out.bam		ENCORE2	18233
SF3B2-BGKcLV33-52_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	2066					GRCh38	V40	SF3B2-BGKcLV33-52/Aligned.sortedByCoord.out.bam		ENCORE2	18289
SF3B2-BGKcLV33-52_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	2066					GRCh38	V40	SF3B2-BGKcLV33-52/Aligned.sortedByCoord.out.bam		ENCORE2	18345
SF3B2-BGKcLV33-52_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2066					GRCh38	V40	SF3B2-BGKcLV33-52_S92_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B2-BGKcLV33-52_S92_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18401