SMG7 RNA-Seq in K562

General Information


RBP	SMG7
Cell_Line	K562
Method	CRISPR
Exp_Name	SMG7-BGKcLV33-K562
ENCODE_series_ID	ENCSR871SAO
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR157IJG
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SMG7-BGKcLV33-57
Rep2	SMG7-BGKcLV33-58
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	77.8
Rep2_WB	71.8
Antibody Cat#	A302-210A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	910

Experiment Information (Status: Released)

	BGKcLV33-53	BGKcLV33-53	BGKcLV33-54	BGKcLV33-54
idx	1155	1244	1156	1245
TRCN#_or_BGC#	BGC#0000872	BGC#0000866	BGC#0000872	BGC#0000866
shRNA_or_gRNA_sequence	GAAAATGCTAGTTACCGATT	ACGCACTGTCCAGACAGCGT	GAAAATGCTAGTTACCGATT	ACGCACTGTCCAGACAGCGT
PAM	TGG	TGG	TGG	TGG
Name	SMG7_92	SF3B3_90	SMG7_92	SF3B3_90
Sample_ID	BGKcLV33-53	BGKcLV33-53	BGKcLV33-54	BGKcLV33-54
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	SMG7	SF3B3	SMG7	SF3B3
qPCR_result		0.0		11.0
Ave_qPCR		5.5
RT-qPCR_primer-F		cgttcctggccagttcttag
RT-qPCR_primer-R		ccaggggagatgaaatggta
protein_conc	420	2019	470	1900
WB_result	no band on the position	78.4		69.1
Ave_WB		73.7
WB_DONE_date	2/1/22	3/7/22
MW	127kd	136kd
IP
antibody_Cat#	A302-170A	A302-508A	LOT #1	LOT #1
Antibody DCC ID		ENCAB290RUF		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	5302	5393	5303	5394

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SF3B3	Product_ID: A302-508A Lot_ID: 1 Source: Bethyl Labs Target Name: SF3B3-human

Experiment Status

	BGKcLV33-53	BGKcLV33-53	BGKcLV33-54	BGKcLV33-54
Sample_ID	BGKcLV33-53	BGKcLV33-53	BGKcLV33-54	BGKcLV33-54
Sample Name
Sample Name	SF3B3-BGKcLV33-53		SF3B3-BGKcLV33-54
RBP	SF3B3	SMG7	SF3B3	SMG7
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	10669	10739	10670	10740

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-53	BGKcLV33-54
Sample #	39	40
Sample Name	SF3B3-BGKcLV33-53	SF3B3-BGKcLV33-54
Sample_Name_Alias
Index Well Position	G05	H05
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	289	299
Peak_Molarity	53.10	57.70
libSampleQC_DNA_Well	DNA_Library_set53/set1/G9.png	DNA_Library_set53/set1/H9.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set53/set1/G5.png	RNA_Library_set53/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-53	BGKcLV33-54
RBP	SF3B3	SF3B3
Batch_ID	BGKcLV33	BGKcLV33
WB_result	78.400	69.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3300	3301

Sequencing Information

	BGKcLV33-53	BGKcLV33-54
Sample_ID	BGKcLV33-53	BGKcLV33-54
Sample Name	SF3B3-BGKcLV33-53	SF3B3-BGKcLV33-54
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	124,569,244	112,717,024
total_aligned_reads	112,557,122	102,436,242
unique_aligned_reads	103,260,866	94,097,548
percent_uniqueAligned	0.82894	0.83481
correlation_replicates	0.996180	0.996180
spikein_reads	3,670	5,392
percent_spikeins	0.00003	0.00005
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2067	2068

Data Submission Information

	BGKcLV33-53	BGKcLV33-53	BGKcLV33-53	BGKcLV33-53	BGKcLV33-53	BGKcLV33-53	BGKcLV33-54	BGKcLV33-54	BGKcLV33-54	BGKcLV33-54
ENCODE_alias	brenton-graveley:SF3B3-BGKcLV33	brenton-graveley:SF3B3-BGKcLV33-53	brenton-graveley:L-SF3B3-BGKcLV33-53	brenton-graveley:SF3B3-BGKcLV33-53_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3B3-BGKcLV33-53_S93_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3B3-BGKcLV33-K562	brenton-graveley:SF3B3-BGKcLV33-54	brenton-graveley:L-SF3B3-BGKcLV33-54	brenton-graveley:SF3B3-BGKcLV33-54_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SF3B3-BGKcLV33-54_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR034FLW	ENCBS586NYG	ENCLB153BJX	ENCFF172QJK	ENCFF919RCT	ENCSR497ASE	ENCBS612ZRN	ENCLB923DGL	ENCFF888YQJ	ENCFF984EIX
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	BGKcLV33-53	BGKcLV33-53	BGKcLV33-53	BGKcLV33-53	BGKcLV33-53	BGKcLV33-53	BGKcLV33-54	BGKcLV33-54	BGKcLV33-54	BGKcLV33-54
Sample Name	SF3B3-BGKcLV33-53	SF3B3-BGKcLV33-53	SF3B3-BGKcLV33-53	SF3B3-BGKcLV33-53	SF3B3-BGKcLV33-53	SF3B3-BGKcLV33-53	SF3B3-BGKcLV33-54	SF3B3-BGKcLV33-54	SF3B3-BGKcLV33-54	SF3B3-BGKcLV33-54
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		SF3B3-BGKcLV33-53.pdf	L-SF3B3-BGKcLV33-53.pdf				SF3B3-BGKcLV33-54.pdf	L-SF3B3-BGKcLV33-54.pdf
ID	7489	7587	7697	7809	7919	7979	7588	7698	7810	7920

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
SF3B3-BGKcLV33-53_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2067	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	6645
SF3B3-BGKcLV33-53_S93_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2067	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	6701
SF3B3-BGKcLV33-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2067					GRCh38	V40	SF3B3-BGKcLV33-53_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGKcLV33-53_S93_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18122
SF3B3-BGKcLV33-53_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	2067					GRCh38	V40	SF3B3-BGKcLV33-53/Aligned.sortedByCoord.out.bam		ENCORE2	18178
SF3B3-BGKcLV33-53_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	2067					GRCh38	V40	SF3B3-BGKcLV33-53/Aligned.sortedByCoord.out.bam		ENCORE2	18234
SF3B3-BGKcLV33-53_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	2067					GRCh38	V40	SF3B3-BGKcLV33-53/Aligned.sortedByCoord.out.bam		ENCORE2	18290
SF3B3-BGKcLV33-53_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	2067					GRCh38	V40	SF3B3-BGKcLV33-53/Aligned.sortedByCoord.out.bam		ENCORE2	18346
SF3B3-BGKcLV33-53_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2067					GRCh38	V40	SF3B3-BGKcLV33-53_S93_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGKcLV33-53_S93_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18402
SF3B3-BGKcLV33-54_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2068	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	6646
SF3B3-BGKcLV33-54_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2068	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	6702
SF3B3-BGKcLV33-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2068					GRCh38	V40	SF3B3-BGKcLV33-54_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGKcLV33-54_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18123
SF3B3-BGKcLV33-54_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	2068					GRCh38	V40	SF3B3-BGKcLV33-54/Aligned.sortedByCoord.out.bam		ENCORE2	18179
SF3B3-BGKcLV33-54_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	2068					GRCh38	V40	SF3B3-BGKcLV33-54/Aligned.sortedByCoord.out.bam		ENCORE2	18235
SF3B3-BGKcLV33-54_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	2068					GRCh38	V40	SF3B3-BGKcLV33-54/Aligned.sortedByCoord.out.bam		ENCORE2	18291
SF3B3-BGKcLV33-54_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	2068					GRCh38	V40	SF3B3-BGKcLV33-54/Aligned.sortedByCoord.out.bam		ENCORE2	18347
SF3B3-BGKcLV33-54_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2068					GRCh38	V40	SF3B3-BGKcLV33-54_S94_L002_R1_001.filtered.trimmed.paired.fastq.gz,SF3B3-BGKcLV33-54_S94_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18403