SRA1 RNA-Seq in K562

General Information


RBP	SRA1
Cell_Line	K562
Method	CRISPR
Exp_Name	SRA1-BGKcLV33-K562
ENCODE_series_ID	ENCSR458NFA
Batch_ID	BGKcLV33
Pool ID	Pool-220418
Local_Set_Name	set53
ENCODE_KD_Exp_ID	ENCSR033MIV
ENCODE_CN_Exp_ID	ENCSR271ZAB
Rep1	SRA1-BGKcLV33-73
Rep2	SRA1-BGKcLV33-74
CN1	NT-BGKcLV33-1
CN2	NT-BGKcLV33-2
Rep1_qPCR	35.7
Rep2_qPCR	43.4
Rep1_WB	82.7
Rep2_WB	80.6
Antibody Cat#	A300-743A
Antibody Lot#	LOT #1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCODE4
ID	916

Experiment Information (Status: Released)

	BGKcLV33-69	BGKcLV33-69	BGKcLV33-69	BGKcLV33-70	BGKcLV33-70	BGKcLV33-70
idx	1171	1266	1268	1172	1267	1269
TRCN#_or_BGC#	BGC#0000887	BGC#0000884	BGC#0000884	BGC#0000887	BGC#0000884	BGC#0000884
shRNA_or_gRNA_sequence	GCGCTCGCTGCTTACCAAGA	TCCCTGGGCCAGTACGGTAT	TCCCTGGGCCAGTACGGTAT	GCGCTCGCTGCTTACCAAGA	TCCCTGGGCCAGTACGGTAT	TCCCTGGGCCAGTACGGTAT
PAM	GGG	TGG	TGG	GGG	TGG	TGG
Name	SRA1_93	SPATS2_97	SPATS2_97	SRA1_93	SPATS2_97	SPATS2_97
Sample_ID	BGKcLV33-69	BGKcLV33-69	BGKcLV33-69	BGKcLV33-70	BGKcLV33-70	BGKcLV33-70
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	SRA1	SPATS2	SPATS2	SRA1	SPATS2	SPATS2
qPCR_result		XX	xx		XX	xx
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	426	2430	2430	374	2215	2215
WB_result	53.3	87.5	not as good as A304-970A, more non-sepcific bands	50.8	80.4
Ave_WB	52.1	83.9
WB_DONE_date	2/2/22	3/10/22	4/18/22
MW	26kd	60kd	60kd
IP
antibody_Cat#	A300-743A	A304-970A	A304-971A	LOT #1	LOT #1	LOT #1
Antibody DCC ID		ENCAB243SMV			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	5311	5408	5410	5312	5409	5411

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SPATS2	Product_ID: A304-970A Lot_ID: 1 Source: Bethyl Labs Target Name: SPATS2-human

Experiment Status

	BGKcLV33-69	BGKcLV33-69	BGKcLV33-70	BGKcLV33-70
Sample_ID	BGKcLV33-69	BGKcLV33-69	BGKcLV33-70	BGKcLV33-70
Sample Name
Sample Name	SPATS2-BGKcLV33-69		SPATS2-BGKcLV33-70
RBP	SPATS2	SRA1	SPATS2	SRA1
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	10683	10755	10684	10756

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-69	BGKcLV33-70
Sample #	53	54
Sample Name	SPATS2-BGKcLV33-69	SPATS2-BGKcLV33-70
Sample_Name_Alias
Index Well Position	E07	F07
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	296	295
Peak_Molarity	69.90	71.30
libSampleQC_DNA_Well	DNA_Library_set53/set1/E11.png	DNA_Library_set53/set1/F11.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set53/set1/E7.png	RNA_Library_set53/set1/F7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-69	BGKcLV33-70
RBP	SPATS2	SPATS2
Batch_ID	BGKcLV33	BGKcLV33
WB_result	87.500	80.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3314	3315

Sequencing Information

	BGKcLV33-69	BGKcLV33-70
Sample_ID	BGKcLV33-69	BGKcLV33-70
Sample Name	SPATS2-BGKcLV33-69	SPATS2-BGKcLV33-70
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	121,886,858	112,819,802
total_aligned_reads	111,478,812	103,295,086
unique_aligned_reads	102,331,786	94,757,030
percent_uniqueAligned	0.83956	0.83990
correlation_replicates	0.998041	0.998041
spikein_reads	9,086	4,468
percent_spikeins	0.00007	0.00004
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2081	2082

Data Submission Information

	BGKcLV33-69	BGKcLV33-69	BGKcLV33-69	BGKcLV33-69	BGKcLV33-69	BGKcLV33-69	BGKcLV33-70	BGKcLV33-70	BGKcLV33-70	BGKcLV33-70
ENCODE_alias	brenton-graveley:SPATS2-BGKcLV33	brenton-graveley:SPATS2-BGKcLV33-69	brenton-graveley:L-SPATS2-BGKcLV33-69	brenton-graveley:SPATS2-BGKcLV33-69_S107_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SPATS2-BGKcLV33-69_S107_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SPATS2-BGKcLV33-K562	brenton-graveley:SPATS2-BGKcLV33-70	brenton-graveley:L-SPATS2-BGKcLV33-70	brenton-graveley:SPATS2-BGKcLV33-70_S108_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SPATS2-BGKcLV33-70_S108_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR535TPQ	ENCBS228HSK	ENCLB264ENU	ENCFF326BVT	ENCFF838JBD	ENCSR823WFJ	ENCBS312MQH	ENCLB389NKG	ENCFF638UGZ	ENCFF712GGZ
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	BGKcLV33-69	BGKcLV33-69	BGKcLV33-69	BGKcLV33-69	BGKcLV33-69	BGKcLV33-69	BGKcLV33-70	BGKcLV33-70	BGKcLV33-70	BGKcLV33-70
Sample Name	SPATS2-BGKcLV33-69	SPATS2-BGKcLV33-69	SPATS2-BGKcLV33-69	SPATS2-BGKcLV33-69	SPATS2-BGKcLV33-69	SPATS2-BGKcLV33-69	SPATS2-BGKcLV33-70	SPATS2-BGKcLV33-70	SPATS2-BGKcLV33-70	SPATS2-BGKcLV33-70
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		SPATS2-BGKcLV33-69.pdf	L-SPATS2-BGKcLV33-69.pdf				SPATS2-BGKcLV33-70.pdf	L-SPATS2-BGKcLV33-70.pdf
ID	7496	7601	7711	7823	7933	7986	7602	7712	7824	7934

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
SPATS2-BGKcLV33-69_S107_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2081	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	6661
SPATS2-BGKcLV33-69_S107_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2081	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	6717
SPATS2-BGKcLV33-69_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2081					GRCh38	V40	SPATS2-BGKcLV33-69_S107_L002_R1_001.filtered.trimmed.paired.fastq.gz,SPATS2-BGKcLV33-69_S107_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18138
SPATS2-BGKcLV33-69_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	2081					GRCh38	V40	SPATS2-BGKcLV33-69/Aligned.sortedByCoord.out.bam		ENCORE2	18194
SPATS2-BGKcLV33-69_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	2081					GRCh38	V40	SPATS2-BGKcLV33-69/Aligned.sortedByCoord.out.bam		ENCORE2	18250
SPATS2-BGKcLV33-69_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	2081					GRCh38	V40	SPATS2-BGKcLV33-69/Aligned.sortedByCoord.out.bam		ENCORE2	18306
SPATS2-BGKcLV33-69_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	2081					GRCh38	V40	SPATS2-BGKcLV33-69/Aligned.sortedByCoord.out.bam		ENCORE2	18362
SPATS2-BGKcLV33-69_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2081					GRCh38	V40	SPATS2-BGKcLV33-69_S107_L002_R1_001.filtered.trimmed.paired.fastq.gz,SPATS2-BGKcLV33-69_S107_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18418
SPATS2-BGKcLV33-70_S108_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2082	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	6662
SPATS2-BGKcLV33-70_S108_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2082	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	6718
SPATS2-BGKcLV33-70_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2082					GRCh38	V40	SPATS2-BGKcLV33-70_S108_L002_R1_001.filtered.trimmed.paired.fastq.gz,SPATS2-BGKcLV33-70_S108_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18139
SPATS2-BGKcLV33-70_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	2082					GRCh38	V40	SPATS2-BGKcLV33-70/Aligned.sortedByCoord.out.bam		ENCORE2	18195
SPATS2-BGKcLV33-70_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	2082					GRCh38	V40	SPATS2-BGKcLV33-70/Aligned.sortedByCoord.out.bam		ENCORE2	18251
SPATS2-BGKcLV33-70_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	2082					GRCh38	V40	SPATS2-BGKcLV33-70/Aligned.sortedByCoord.out.bam		ENCORE2	18307
SPATS2-BGKcLV33-70_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	2082					GRCh38	V40	SPATS2-BGKcLV33-70/Aligned.sortedByCoord.out.bam		ENCORE2	18363
SPATS2-BGKcLV33-70_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2082					GRCh38	V40	SPATS2-BGKcLV33-70_S108_L002_R1_001.filtered.trimmed.paired.fastq.gz,SPATS2-BGKcLV33-70_S108_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18419