SF3B2 RNA-Seq in K562

General Information


RBP	SF3B2
Cell_Line	K562
Method	CRISPR
Exp_Name	SF3B2-BGKcLV33-K562
ENCODE_series_ID	ENCSR292ATE
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR447ARO
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SF3B2-BGKcLV33-51
Rep2	SF3B2-BGKcLV33-52
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	no band on the position
Rep2_WB
Antibody Cat#	A302-804A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	907

Experiment Information (Status: Released)

	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-46	BGKcLV33-46	BGKcLV33-46
idx	1147	1232	1234	1148	1233	1235
TRCN#_or_BGC#	BGC#0000863	BGC#0000858	BGC#0000858	BGC#0000863	BGC#0000858	BGC#0000858
shRNA_or_gRNA_sequence	TGGCATCGTGCTGAATCGGC	AAATCCCACGGTGTCAACAA	AAATCCCACGGTGTCAACAA	TGGCATCGTGCTGAATCGGC	AAATCCCACGGTGTCAACAA	AAATCCCACGGTGTCAACAA
PAM	CGG	TGG	TGG	CGG	TGG	TGG
Name	SF3B2_94	SEPTIN11_86	SEPTIN11_86	SF3B2_94	SEPTIN11_86	SEPTIN11_86
Sample_ID	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-46	BGKcLV33-46	BGKcLV33-46
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	SF3B2	SEPT11	SEPT11	SF3B2	SEPT11	SEPT11
qPCR_result		65.0	65.0		50.4	50.4
Ave_qPCR		57.7	57.7
RT-qPCR_primer-F		actgaccctgacagcaaacc	actgaccctgacagcaaacc
RT-qPCR_primer-R		tctgcagttctcccaggaat	tctgcagttctcccaggaat
protein_conc	417	2327	2327	404	2430	2430
WB_result	95.5	77.4	81.6	97.0	80.8	81.5
Ave_WB	96.2	79.1	81.5
WB_DONE_date	1/26/22	3/14/22	3/23/22
MW	100kd	49kd	49kd
IP
antibody_Cat#	A301-605A	A304-176A	A304-177A	LOT #1	LOT #1	LOT #1
Antibody DCC ID		NO ID	NO ID		8/4/22	8/4/22
submitted_to_DCC_date
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	5287	5374	5376	5288	5375	5377

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SEPT11	Product_ID: A304-176A Lot_ID: 1 Source: Bethyl Labs Target Name: SEPT11-human
SEPT11	Product_ID: A304-177A Lot_ID: 1 Source: Bethyl Labs Target Name: SEPT11-human

Experiment Status

	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-46	BGKcLV33-46	BGKcLV33-46
Sample_ID	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-46	BGKcLV33-46	BGKcLV33-46
Sample Name				SEPT11-BGKcLV33-46
Sample Name	SEPT11-BGKcLV33-45			SEPT11-BGKcLV33-46
RBP	SEPT11	SF3B2	SEPT11	SEPT11	SF3B2	SEPT11
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				RNU6-644P FPKM was 38600300. Correlation between SEPT11-BGKcLV33-45 and SEPT11-BGKcLV33-46 is 0.000699976. After set RNU6-644P value to 0, the Correlation between SEPT11-BGKcLV33-45 and SEPT11-BGKcLV33-46 is 0.9926758. Furthermore, 0.9875285 was got using salmon counts.
ID	10663	10731	10781	10664	10732	10782

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-45	BGKcLV33-46
Sample #	33	34
Sample Name	SEPT11-BGKcLV33-45	SEPT11-BGKcLV33-46
Sample_Name_Alias
Index Well Position	A05	B05
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	294	289
Peak_Molarity	60.80	54.60
libSampleQC_DNA_Well	DNA_Library_set53/set1/A9.png	DNA_Library_set53/set1/B9.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set53/set1/A5.png	RNA_Library_set53/set1/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-45	BGKcLV33-46
RBP	SEPT11	SEPT11
Batch_ID	BGKcLV33	BGKcLV33
WB_result	77.400	80.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3294	3295

Sequencing Information

	BGKcLV33-45	BGKcLV33-46
Sample_ID	BGKcLV33-45	BGKcLV33-46
Sample Name	SEPT11-BGKcLV33-45	SEPT11-BGKcLV33-46
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	107,766,898	113,819,980
total_aligned_reads	100,298,424	105,690,406
unique_aligned_reads	91,985,188	96,542,856
percent_uniqueAligned	0.85356	0.84821
correlation_replicates	0.992676	0.992676
spikein_reads	20,560	18,146
percent_spikeins	0.00019	0.00016
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2061	2062

Data Submission Information

	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-46	BGKcLV33-46	BGKcLV33-46	BGKcLV33-46
ENCODE_alias	brenton-graveley:SEPT11-BGKcLV33	brenton-graveley:SEPT11-BGKcLV33-45	brenton-graveley:L-SEPT11-BGKcLV33-45	brenton-graveley:SEPT11-BGKcLV33-45_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEPT11-BGKcLV33-45_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEPT11-BGKcLV33-K562	brenton-graveley:SEPT11-BGKcLV33-46	brenton-graveley:L-SEPT11-BGKcLV33-46	brenton-graveley:SEPT11-BGKcLV33-46_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEPT11-BGKcLV33-46_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR727WPW	ENCBS765CBQ	ENCLB252HGZ	ENCFF118ODS	ENCFF761VST	ENCSR562ZCK	ENCBS347VSX	ENCLB247HXV	ENCFF836PAB	ENCFF138CLJ
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	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-45	BGKcLV33-46	BGKcLV33-46	BGKcLV33-46	BGKcLV33-46
Sample Name	SEPT11-BGKcLV33-45	SEPT11-BGKcLV33-45	SEPT11-BGKcLV33-45	SEPT11-BGKcLV33-45	SEPT11-BGKcLV33-45	SEPT11-BGKcLV33-45	SEPT11-BGKcLV33-46	SEPT11-BGKcLV33-46	SEPT11-BGKcLV33-46	SEPT11-BGKcLV33-46
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		SEPT11-BGKcLV33-45.pdf	L-SEPT11-BGKcLV33-45.pdf				SEPT11-BGKcLV33-46.pdf	L-SEPT11-BGKcLV33-46.pdf
ID	7498	7605	7715	7803	7913	7976	7606	7716	7804	7914

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
SEPT11-BGKcLV33-45_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2061	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	6639
SEPT11-BGKcLV33-45_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2061	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	6695
SEPT11-BGKcLV33-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2061					GRCh38	V40	SEPT11-BGKcLV33-45_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEPT11-BGKcLV33-45_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18116
SEPT11-BGKcLV33-45_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	2061					GRCh38	V40	SEPT11-BGKcLV33-45/Aligned.sortedByCoord.out.bam		ENCORE2	18172
SEPT11-BGKcLV33-45_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	2061					GRCh38	V40	SEPT11-BGKcLV33-45/Aligned.sortedByCoord.out.bam		ENCORE2	18228
SEPT11-BGKcLV33-45_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	2061					GRCh38	V40	SEPT11-BGKcLV33-45/Aligned.sortedByCoord.out.bam		ENCORE2	18284
SEPT11-BGKcLV33-45_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	2061					GRCh38	V40	SEPT11-BGKcLV33-45/Aligned.sortedByCoord.out.bam		ENCORE2	18340
SEPT11-BGKcLV33-45_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2061					GRCh38	V40	SEPT11-BGKcLV33-45_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEPT11-BGKcLV33-45_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18396
SEPT11-BGKcLV33-46_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2062	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	6640
SEPT11-BGKcLV33-46_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2062	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	6696
SEPT11-BGKcLV33-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2062					GRCh38	V40	SEPT11-BGKcLV33-46_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEPT11-BGKcLV33-46_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18117
SEPT11-BGKcLV33-46_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	2062					GRCh38	V40	SEPT11-BGKcLV33-46/Aligned.sortedByCoord.out.bam		ENCORE2	18173
SEPT11-BGKcLV33-46_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	2062					GRCh38	V40	SEPT11-BGKcLV33-46/Aligned.sortedByCoord.out.bam		ENCORE2	18229
SEPT11-BGKcLV33-46_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	2062					GRCh38	V40	SEPT11-BGKcLV33-46/Aligned.sortedByCoord.out.bam		ENCORE2	18285
SEPT11-BGKcLV33-46_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	2062					GRCh38	V40	SEPT11-BGKcLV33-46/Aligned.sortedByCoord.out.bam		ENCORE2	18341
SEPT11-BGKcLV33-46_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2062					GRCh38	V40	SEPT11-BGKcLV33-46_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEPT11-BGKcLV33-46_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18397