SEC23IP RNA-Seq in K562

Experiment Information (Status: Released)

	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-30	BGKcLV33-30	BGKcLV33-30
idx	1131	1210	1212	1132	1211	1213
TRCN#_or_BGC#	BGC#0000848	BGC#0000842	BGC#0000842	BGC#0000848	BGC#0000842	BGC#0000842
shRNA_or_gRNA_sequence	GCCGAGAGAAAACCTAACGG	GTCGTCTCTCGCAGTTTACG	GTCGTCTCTCGCAGTTTACG	GCCGAGAGAAAACCTAACGG	GTCGTCTCTCGCAGTTTACG	GTCGTCTCTCGCAGTTTACG
PAM	TGG	CGG	CGG	TGG	CGG	CGG
Name	SEC23IP_96	SAP30BP_97	SAP30BP_97	SEC23IP_96	SAP30BP_97	SAP30BP_97
Sample_ID	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-30	BGKcLV33-30	BGKcLV33-30
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	SEC23IP	SAP30BP	SAP30BP	SEC23IP	SAP30BP	SAP30BP
qPCR_result		0.0	0.0		0.0	0.0
Ave_qPCR		0.0	0.0
RT-qPCR_primer-F		cctggcagatgttcaaatca	cctggcagatgttcaaatca
RT-qPCR_primer-R		gggttccgaaattctttcttc	gggttccgaaattctttcttc
protein_conc	371	2034	2034	394	2087	2087
WB_result	no band on the position	71.6	68.2		68.3	79.2533545
Ave_WB		69.9	73.7
WB_DONE_date	1/24/22	3/2/22	3/22/22
MW	111kd	34kd	34kd
IP
antibody_Cat#	A300-592A	A302-832A	A302-833A	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	5271	5352	5354	5272	5353	5355

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SAP30BP	Product_ID: A302-832A Lot_ID: 1 Source: Bethyl Labs Target Name: SAP30BP-human
SAP30BP	Product_ID: A302-833A Lot_ID: 1 Source: Bethyl Labs Target Name: SAP30BP-human

Experiment Status

	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-30	BGKcLV33-30	BGKcLV33-30
Sample_ID	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-30	BGKcLV33-30	BGKcLV33-30
Sample Name
Sample Name	SAP30BP-BGKcLV33-29			SAP30BP-BGKcLV33-30
RBP	SAP30BP	SEC23IP	SAP30BP	SAP30BP	SEC23IP	SAP30BP
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	10651	10715	10771	10652	10716	10772

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-29	BGKcLV33-30
Sample #	21	22
Sample Name	SAP30BP-BGKcLV33-29	SAP30BP-BGKcLV33-30
Sample_Name_Alias
Index Well Position	E03	F03
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	290
Peak_Molarity	55.10	66.10
libSampleQC_DNA_Well	DNA_Library_set53/set1/E7.png	DNA_Library_set53/set1/F7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set53/set1/E3.png	RNA_Library_set53/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-29	BGKcLV33-30
RBP	SAP30BP	SAP30BP
Batch_ID	BGKcLV33	BGKcLV33
WB_result	71.600	68.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3282	3283

Sequencing Information

	BGKcLV33-29	BGKcLV33-30
Sample_ID	BGKcLV33-29	BGKcLV33-30
Sample Name	SAP30BP-BGKcLV33-29	SAP30BP-BGKcLV33-30
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	164,009,540	125,033,682
total_aligned_reads	147,455,920	112,973,394
unique_aligned_reads	135,321,182	103,860,034
percent_uniqueAligned	0.82508	0.83066
correlation_replicates	0.998147	0.998147
spikein_reads	8,796	5,780
percent_spikeins	0.00005	0.00005
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2049	2050

Data Submission Information

	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-30	BGKcLV33-30	BGKcLV33-30	BGKcLV33-30
ENCODE_alias	brenton-graveley:SAP30BP-BGKcLV33	brenton-graveley:SAP30BP-BGKcLV33-29	brenton-graveley:L-SAP30BP-BGKcLV33-29	brenton-graveley:SAP30BP-BGKcLV33-29_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAP30BP-BGKcLV33-29_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAP30BP-BGKcLV33-K562	brenton-graveley:SAP30BP-BGKcLV33-30	brenton-graveley:L-SAP30BP-BGKcLV33-30	brenton-graveley:SAP30BP-BGKcLV33-30_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SAP30BP-BGKcLV33-30_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR068YPI	ENCBS042QOZ	ENCLB473BIQ	ENCFF492YAQ	ENCFF567XAE	ENCSR057UBZ	ENCBS312BGW	ENCLB680UED	ENCFF442PMV	ENCFF590XHA
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	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-29	BGKcLV33-30	BGKcLV33-30	BGKcLV33-30	BGKcLV33-30
Sample Name	SAP30BP-BGKcLV33-29	SAP30BP-BGKcLV33-29	SAP30BP-BGKcLV33-29	SAP30BP-BGKcLV33-29	SAP30BP-BGKcLV33-29	SAP30BP-BGKcLV33-29	SAP30BP-BGKcLV33-30	SAP30BP-BGKcLV33-30	SAP30BP-BGKcLV33-30	SAP30BP-BGKcLV33-30
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		SAP30BP-BGKcLV33-29.pdf	L-SAP30BP-BGKcLV33-29.pdf				SAP30BP-BGKcLV33-30.pdf	L-SAP30BP-BGKcLV33-30.pdf
ID	7481	7571	7681	7791	7901	7970	7572	7682	7792	7902

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
SAP30BP-BGKcLV33-29_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2049	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	6627
SAP30BP-BGKcLV33-29_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2049	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	6683
SAP30BP-BGKcLV33-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2049					GRCh38	V40	SAP30BP-BGKcLV33-29_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz,SAP30BP-BGKcLV33-29_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18104
SAP30BP-BGKcLV33-29_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	2049					GRCh38	V40	SAP30BP-BGKcLV33-29/Aligned.sortedByCoord.out.bam		ENCORE2	18160
SAP30BP-BGKcLV33-29_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	2049					GRCh38	V40	SAP30BP-BGKcLV33-29/Aligned.sortedByCoord.out.bam		ENCORE2	18216
SAP30BP-BGKcLV33-29_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	2049					GRCh38	V40	SAP30BP-BGKcLV33-29/Aligned.sortedByCoord.out.bam		ENCORE2	18272
SAP30BP-BGKcLV33-29_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	2049					GRCh38	V40	SAP30BP-BGKcLV33-29/Aligned.sortedByCoord.out.bam		ENCORE2	18328
SAP30BP-BGKcLV33-29_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2049					GRCh38	V40	SAP30BP-BGKcLV33-29_S75_L002_R1_001.filtered.trimmed.paired.fastq.gz,SAP30BP-BGKcLV33-29_S75_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18384
SAP30BP-BGKcLV33-30_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2050	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	6628
SAP30BP-BGKcLV33-30_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2050	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	6684
SAP30BP-BGKcLV33-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2050					GRCh38	V40	SAP30BP-BGKcLV33-30_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz,SAP30BP-BGKcLV33-30_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18105
SAP30BP-BGKcLV33-30_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	2050					GRCh38	V40	SAP30BP-BGKcLV33-30/Aligned.sortedByCoord.out.bam		ENCORE2	18161
SAP30BP-BGKcLV33-30_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	2050					GRCh38	V40	SAP30BP-BGKcLV33-30/Aligned.sortedByCoord.out.bam		ENCORE2	18217
SAP30BP-BGKcLV33-30_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	2050					GRCh38	V40	SAP30BP-BGKcLV33-30/Aligned.sortedByCoord.out.bam		ENCORE2	18273
SAP30BP-BGKcLV33-30_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	2050					GRCh38	V40	SAP30BP-BGKcLV33-30/Aligned.sortedByCoord.out.bam		ENCORE2	18329
SAP30BP-BGKcLV33-30_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2050					GRCh38	V40	SAP30BP-BGKcLV33-30_S76_L002_R1_001.filtered.trimmed.paired.fastq.gz,SAP30BP-BGKcLV33-30_S76_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18385