SPATS2 RNA-Seq in K562

General Information


RBP	SPATS2
Cell_Line	K562
Method	CRISPR
Exp_Name	SPATS2-BGKcLV33-K562
ENCODE_series_ID	ENCSR823WFJ
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR535TPQ
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SPATS2-BGKcLV33-69
Rep2	SPATS2-BGKcLV33-70
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	53.3
Rep2_WB	50.8
Antibody Cat#	A300-743A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	915

Experiment Information (Status: Released)

	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-66	BGKcLV33-66	BGKcLV33-66
idx	1167	1258	1260	1168	1259	1261
TRCN#_or_BGC#	BGC#0000883	BGC#0000879	BGC#0000879	BGC#0000883	BGC#0000879	BGC#0000879
shRNA_or_gRNA_sequence	TCGAAGAAACGACAATGTCC	TCATACCGGATATACTGAGC	TCATACCGGATATACTGAGC	TCGAAGAAACGACAATGTCC	TCATACCGGATATACTGAGC	TCATACCGGATATACTGAGC
PAM	AGG	AGG	AGG	AGG	AGG	AGG
Name	SPATS2_86	SNW1_93	SNW1_93	SPATS2_86	SNW1_93	SNW1_93
Sample_ID	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-66	BGKcLV33-66	BGKcLV33-66
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	SPATS2	SNW1	SNW1	SPATS2	SNW1	SNW1
qPCR_result		40.5	40.5		46.7	46.7
Ave_qPCR		43.6	43.6
RT-qPCR_primer-F		ggaccaccttctcctcctg	ggaccaccttctcctcctg
RT-qPCR_primer-R		ggaggaatcttccactcttgtt	ggaggaatcttccactcttgtt
protein_conc	404	2157	2157	444	2094	2094
WB_result	no band on the position	97.1	95.4		94.9	93.8742637
Ave_WB		96.0	94.6
WB_DONE_date	2/1/22	3/16/22	3/22/22
MW	60kd	61kd	61kd
IP
antibody_Cat#	A304-970A	A300-785A	A300-784A	LOT #1	LOT #1	LOT #1
Antibody DCC ID		ENCAB440BLE	ENCAB574RLF		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	5307	5400	5402	5308	5401	5403

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SNW1	Product_ID: A300-785A Lot_ID: 1 Source: Bethyl Labs Target Name: SNW1-human
SNW1	Product_ID: A300-784A Lot_ID: 1 Source: Bethyl Labs Target Name: SNW1-human

Experiment Status

	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-66	BGKcLV33-66	BGKcLV33-66
Sample_ID	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-66	BGKcLV33-66	BGKcLV33-66
Sample Name
Sample Name	SNW1-BGKcLV33-65			SNW1-BGKcLV33-66
RBP	SNW1	SPATS2	SNW1	SNW1	SPATS2	SNW1
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	10679	10751	10789	10680	10752	10790

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-65	BGKcLV33-66
Sample #	49	50
Sample Name	SNW1-BGKcLV33-65	SNW1-BGKcLV33-66
Sample_Name_Alias
Index Well Position	A07	B07
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	299	298
Peak_Molarity	64.50	73.40
libSampleQC_DNA_Well	DNA_Library_set53/set1/A11.png	DNA_Library_set53/set1/B11.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set53/set1/A7.png	RNA_Library_set53/set1/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-65	BGKcLV33-66
RBP	SNW1	SNW1
Batch_ID	BGKcLV33	BGKcLV33
WB_result	97.100	94.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3310	3311

Sequencing Information

	BGKcLV33-65	BGKcLV33-66
Sample_ID	BGKcLV33-65	BGKcLV33-66
Sample Name	SNW1-BGKcLV33-65	SNW1-BGKcLV33-66
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	199,471,690	136,942,116
total_aligned_reads	181,974,998	125,892,252
unique_aligned_reads	167,486,444	116,096,092
percent_uniqueAligned	0.83965	0.84777
correlation_replicates	0.996925	0.996925
spikein_reads	36,388	13,064
percent_spikeins	0.00018	0.00010
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2077	2078

Data Submission Information

	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-66	BGKcLV33-66	BGKcLV33-66	BGKcLV33-66
ENCODE_alias	brenton-graveley:SNW1-BGKcLV33	brenton-graveley:SNW1-BGKcLV33-65	brenton-graveley:L-SNW1-BGKcLV33-65	brenton-graveley:SNW1-BGKcLV33-65_S103_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SNW1-BGKcLV33-65_S103_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SNW1-BGKcLV33-K562	brenton-graveley:SNW1-BGKcLV33-66	brenton-graveley:L-SNW1-BGKcLV33-66	brenton-graveley:SNW1-BGKcLV33-66_S104_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SNW1-BGKcLV33-66_S104_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR458FLK	ENCBS949WGL	ENCLB244MGT	ENCFF592XFA	ENCFF113BRV	ENCSR019QSE	ENCBS283NSB	ENCLB077XMO	ENCFF337LRS	ENCFF733WKL
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	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-65	BGKcLV33-66	BGKcLV33-66	BGKcLV33-66	BGKcLV33-66
Sample Name	SNW1-BGKcLV33-65	SNW1-BGKcLV33-65	SNW1-BGKcLV33-65	SNW1-BGKcLV33-65	SNW1-BGKcLV33-65	SNW1-BGKcLV33-65	SNW1-BGKcLV33-66	SNW1-BGKcLV33-66	SNW1-BGKcLV33-66	SNW1-BGKcLV33-66
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		SNW1-BGKcLV33-65.pdf	L-SNW1-BGKcLV33-65.pdf				SNW1-BGKcLV33-66.pdf	L-SNW1-BGKcLV33-66.pdf
ID	7494	7597	7707	7819	7929	7984	7598	7708	7820	7930

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
SNW1-BGKcLV33-65_S103_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2077	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	6657
SNW1-BGKcLV33-65_S103_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2077	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	6713
SNW1-BGKcLV33-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2077					GRCh38	V40	SNW1-BGKcLV33-65_S103_L002_R1_001.filtered.trimmed.paired.fastq.gz,SNW1-BGKcLV33-65_S103_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18134
SNW1-BGKcLV33-65_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	2077					GRCh38	V40	SNW1-BGKcLV33-65/Aligned.sortedByCoord.out.bam		ENCORE2	18190
SNW1-BGKcLV33-65_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	2077					GRCh38	V40	SNW1-BGKcLV33-65/Aligned.sortedByCoord.out.bam		ENCORE2	18246
SNW1-BGKcLV33-65_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	2077					GRCh38	V40	SNW1-BGKcLV33-65/Aligned.sortedByCoord.out.bam		ENCORE2	18302
SNW1-BGKcLV33-65_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	2077					GRCh38	V40	SNW1-BGKcLV33-65/Aligned.sortedByCoord.out.bam		ENCORE2	18358
SNW1-BGKcLV33-65_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2077					GRCh38	V40	SNW1-BGKcLV33-65_S103_L002_R1_001.filtered.trimmed.paired.fastq.gz,SNW1-BGKcLV33-65_S103_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18414
SNW1-BGKcLV33-66_S104_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2078	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	6658
SNW1-BGKcLV33-66_S104_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2078	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	6714
SNW1-BGKcLV33-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2078					GRCh38	V40	SNW1-BGKcLV33-66_S104_L002_R1_001.filtered.trimmed.paired.fastq.gz,SNW1-BGKcLV33-66_S104_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18135
SNW1-BGKcLV33-66_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	2078					GRCh38	V40	SNW1-BGKcLV33-66/Aligned.sortedByCoord.out.bam		ENCORE2	18191
SNW1-BGKcLV33-66_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	2078					GRCh38	V40	SNW1-BGKcLV33-66/Aligned.sortedByCoord.out.bam		ENCORE2	18247
SNW1-BGKcLV33-66_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	2078					GRCh38	V40	SNW1-BGKcLV33-66/Aligned.sortedByCoord.out.bam		ENCORE2	18303
SNW1-BGKcLV33-66_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	2078					GRCh38	V40	SNW1-BGKcLV33-66/Aligned.sortedByCoord.out.bam		ENCORE2	18359
SNW1-BGKcLV33-66_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2078					GRCh38	V40	SNW1-BGKcLV33-66_S104_L002_R1_001.filtered.trimmed.paired.fastq.gz,SNW1-BGKcLV33-66_S104_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18415