SPATS2L RNA-Seq in K562

Experiment Information (Status: Released)

	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-68	BGKcLV33-68	BGKcLV33-68
idx	1169	1262	1264	1170	1263	1265
TRCN#_or_BGC#	BGC#0000885	BGC#0000881	BGC#0000881	BGC#0000885	BGC#0000881	BGC#0000881
shRNA_or_gRNA_sequence	ATCGAGATCTTTTTCTCACG	TATCGGGCGCTATGACGAGG	TATCGGGCGCTATGACGAGG	ATCGAGATCTTTTTCTCACG	TATCGGGCGCTATGACGAGG	TATCGGGCGCTATGACGAGG
PAM	AGG	AGG	AGG	AGG	AGG	AGG
Name	SPATS2L_90	SPAG9_98	SPAG9_98	SPATS2L_90	SPAG9_98	SPAG9_98
Sample_ID	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-68	BGKcLV33-68	BGKcLV33-68
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	SPATS2L	SPAG9	SPAG9	SPATS2L	SPAG9	SPAG9
qPCR_result		34.6	34.6		32.5	32.5
Ave_qPCR		33.6	33.6
RT-qPCR_primer-F		cacccttgcaatctttcaca	cacccttgcaatctttcaca
RT-qPCR_primer-R		agtcatgcaacggatggaat	agtcatgcaacggatggaat
protein_conc	424	2302	2302	390	2526	2526
WB_result	no band on the position	81.3	64.5		77.5	73.5475939
Ave_WB		79.4	69.0
WB_DONE_date	2/1/22	3/10/22	3/16/22
MW	62kd	146kd	146kd
IP
antibody_Cat#	A305-118A	A300-336A	A300-337A	LOT #1	LOT #4	LOT #2
Antibody DCC ID		ENCAB002WNS	ENCAB167KJP
submitted_to_DCC_date		8/16/22	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	5309	5404	5406	5310	5405	5407

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SPAG9	Product_ID: A300-336A Lot_ID: 4 Source: Bethyl Labs Target Name: SPAG9-human
SPAG9	Product_ID: A300-337A Lot_ID: 2 Source: Bethyl Labs Target Name: SPAG9-human

Experiment Status

	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-68	BGKcLV33-68	BGKcLV33-68
Sample_ID	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-68	BGKcLV33-68	BGKcLV33-68
Sample Name
Sample Name	SPAG9-BGKcLV33-67			SPAG9-BGKcLV33-68
RBP	SPAG9	SPATS2L	SPAG9	SPAG9	SPATS2L	SPAG9
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	10681	10753	10791	10682	10754	10792

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-67	BGKcLV33-68
Sample #	51	52
Sample Name	SPAG9-BGKcLV33-67	SPAG9-BGKcLV33-68
Sample_Name_Alias
Index Well Position	C07	D07
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	290	301
Peak_Molarity	73.30	65.60
libSampleQC_DNA_Well	DNA_Library_set53/set1/C11.png	DNA_Library_set53/set1/D11.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set53/set1/C7.png	RNA_Library_set53/set1/D7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-67	BGKcLV33-68
RBP	SPAG9	SPAG9
Batch_ID	BGKcLV33	BGKcLV33
WB_result	81.300	77.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3312	3313

Sequencing Information

	BGKcLV33-67	BGKcLV33-68
Sample_ID	BGKcLV33-67	BGKcLV33-68
Sample Name	SPAG9-BGKcLV33-67	SPAG9-BGKcLV33-68
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	133,667,434	119,391,704
total_aligned_reads	121,576,984	111,221,658
unique_aligned_reads	111,857,358	101,993,406
percent_uniqueAligned	0.83683	0.85428
correlation_replicates	0.996177	0.996177
spikein_reads	9,912	5,308
percent_spikeins	0.00007	0.00004
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2079	2080

Data Submission Information

	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-68	BGKcLV33-68	BGKcLV33-68	BGKcLV33-68
ENCODE_alias	brenton-graveley:SPAG9-BGKcLV33	brenton-graveley:SPAG9-BGKcLV33-67	brenton-graveley:L-SPAG9-BGKcLV33-67	brenton-graveley:SPAG9-BGKcLV33-67_S105_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SPAG9-BGKcLV33-67_S105_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SPAG9-BGKcLV33-K562	brenton-graveley:SPAG9-BGKcLV33-68	brenton-graveley:L-SPAG9-BGKcLV33-68	brenton-graveley:SPAG9-BGKcLV33-68_S106_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SPAG9-BGKcLV33-68_S106_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR642LZB	ENCBS885LGM	ENCLB042VFP	ENCFF541ISK	ENCFF617IJL	ENCSR495FVC	ENCBS390WRH	ENCLB769HXE	ENCFF338FVO	ENCFF121GVN
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	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-67	BGKcLV33-68	BGKcLV33-68	BGKcLV33-68	BGKcLV33-68
Sample Name	SPAG9-BGKcLV33-67	SPAG9-BGKcLV33-67	SPAG9-BGKcLV33-67	SPAG9-BGKcLV33-67	SPAG9-BGKcLV33-67	SPAG9-BGKcLV33-67	SPAG9-BGKcLV33-68	SPAG9-BGKcLV33-68	SPAG9-BGKcLV33-68	SPAG9-BGKcLV33-68
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		SPAG9-BGKcLV33-67.pdf	L-SPAG9-BGKcLV33-67.pdf				SPAG9-BGKcLV33-68.pdf	L-SPAG9-BGKcLV33-68.pdf
ID	7495	7599	7709	7821	7931	7985	7600	7710	7822	7932

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
SPAG9-BGKcLV33-67_S105_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2079	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	6659
SPAG9-BGKcLV33-67_S105_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2079	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	6715
SPAG9-BGKcLV33-67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2079					GRCh38	V40	SPAG9-BGKcLV33-67_S105_L002_R1_001.filtered.trimmed.paired.fastq.gz,SPAG9-BGKcLV33-67_S105_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18136
SPAG9-BGKcLV33-67_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	2079					GRCh38	V40	SPAG9-BGKcLV33-67/Aligned.sortedByCoord.out.bam		ENCORE2	18192
SPAG9-BGKcLV33-67_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	2079					GRCh38	V40	SPAG9-BGKcLV33-67/Aligned.sortedByCoord.out.bam		ENCORE2	18248
SPAG9-BGKcLV33-67_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	2079					GRCh38	V40	SPAG9-BGKcLV33-67/Aligned.sortedByCoord.out.bam		ENCORE2	18304
SPAG9-BGKcLV33-67_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	2079					GRCh38	V40	SPAG9-BGKcLV33-67/Aligned.sortedByCoord.out.bam		ENCORE2	18360
SPAG9-BGKcLV33-67_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2079					GRCh38	V40	SPAG9-BGKcLV33-67_S105_L002_R1_001.filtered.trimmed.paired.fastq.gz,SPAG9-BGKcLV33-67_S105_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18416
SPAG9-BGKcLV33-68_S106_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2080	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	6660
SPAG9-BGKcLV33-68_S106_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2080	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	6716
SPAG9-BGKcLV33-68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2080					GRCh38	V40	SPAG9-BGKcLV33-68_S106_L002_R1_001.filtered.trimmed.paired.fastq.gz,SPAG9-BGKcLV33-68_S106_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18137
SPAG9-BGKcLV33-68_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	2080					GRCh38	V40	SPAG9-BGKcLV33-68/Aligned.sortedByCoord.out.bam		ENCORE2	18193
SPAG9-BGKcLV33-68_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	2080					GRCh38	V40	SPAG9-BGKcLV33-68/Aligned.sortedByCoord.out.bam		ENCORE2	18249
SPAG9-BGKcLV33-68_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	2080					GRCh38	V40	SPAG9-BGKcLV33-68/Aligned.sortedByCoord.out.bam		ENCORE2	18305
SPAG9-BGKcLV33-68_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	2080					GRCh38	V40	SPAG9-BGKcLV33-68/Aligned.sortedByCoord.out.bam		ENCORE2	18361
SPAG9-BGKcLV33-68_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2080					GRCh38	V40	SPAG9-BGKcLV33-68_S106_L002_R1_001.filtered.trimmed.paired.fastq.gz,SPAG9-BGKcLV33-68_S106_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18417