SECISBP2 RNA-Seq in K562

Experiment Information (Status: Released)

	BGKcLV33-37	BGKcLV33-37	BGKcLV33-38	BGKcLV33-38
idx	1139	1224	1140	1225
TRCN#_or_BGC#	BGC#0000856	BGC#0000849	BGC#0000856	BGC#0000849
shRNA_or_gRNA_sequence	GTGACACGTACCTTTTGGGT	AGTGGTGCTTCGATATTCAG	GTGACACGTACCTTTTGGGT	AGTGGTGCTTCGATATTCAG
PAM	AGG	TGG	AGG	TGG
Name	SECISBP2_91	SEC31A_88	SECISBP2_91	SEC31A_88
Sample_ID	BGKcLV33-37	BGKcLV33-37	BGKcLV33-38	BGKcLV33-38
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	SECISBP2	SEC31A	SECISBP2	SEC31A
qPCR_result		46.0		42.6
Ave_qPCR		44.3
RT-qPCR_primer-F		atggcgtacagcaacctctt
RT-qPCR_primer-R		tttgttggcaaagactgcac
protein_conc	342	2171	314	2429
WB_result	no band on the position	79.0		79.0
Ave_WB		79.0
WB_DONE_date	1/24/22	3/16/22
MW	95kd	133kd
IP
antibody_Cat#	A303-949A	A302-336A	LOT #1	LOT #1
Antibody DCC ID		ENCAB110EPA		8/4/22
submitted_to_DCC_date		8/16/22
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action		Ready		Ready
Library_start_date		04/13/22		04/13/22
repeat_library
Note
ID	5279	5366	5280	5367

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SEC31A	Product_ID: A302-336A Lot_ID: 1 Source: Bethyl Labs Target Name: SEC31A-human

Experiment Status

	BGKcLV33-37	BGKcLV33-37	BGKcLV33-38	BGKcLV33-38
Sample_ID	BGKcLV33-37	BGKcLV33-37	BGKcLV33-38	BGKcLV33-38
Sample Name
Sample Name	SEC31A-BGKcLV33-37		SEC31A-BGKcLV33-38
RBP	SEC31A	SECISBP2	SEC31A	SECISBP2
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	10657	10723	10658	10724

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-37	BGKcLV33-38
Sample #	27	28
Sample Name	SEC31A-BGKcLV33-37	SEC31A-BGKcLV33-38
Sample_Name_Alias
Index Well Position	C04	D04
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	71.80	77.90
libSampleQC_DNA_Well	DNA_Library_set53/set1/C8.png	DNA_Library_set53/set1/D8.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set53/set1/C4.png	RNA_Library_set53/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-37	BGKcLV33-38
RBP	SEC31A	SEC31A
Batch_ID	BGKcLV33	BGKcLV33
WB_result	88.400	87.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3288	3289

Sequencing Information

	BGKcLV33-37	BGKcLV33-38
Sample_ID	BGKcLV33-37	BGKcLV33-38
Sample Name	SEC31A-BGKcLV33-37	SEC31A-BGKcLV33-38
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	81,569,266	130,317,598
total_aligned_reads	73,921,856	117,390,326
unique_aligned_reads	67,480,220	107,926,324
percent_uniqueAligned	0.82728	0.82818
correlation_replicates	0.995820	0.995820
spikein_reads	10,728	4,776
percent_spikeins	0.00013	0.00004
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2055	2056

Data Submission Information

	BGKcLV33-37	BGKcLV33-37	BGKcLV33-37	BGKcLV33-37	BGKcLV33-37	BGKcLV33-37	BGKcLV33-38	BGKcLV33-38	BGKcLV33-38	BGKcLV33-38
ENCODE_alias	brenton-graveley:SEC31A-BGKcLV33	brenton-graveley:SEC31A-BGKcLV33-37	brenton-graveley:L-SEC31A-BGKcLV33-37	brenton-graveley:SEC31A-BGKcLV33-37_S81_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC31A-BGKcLV33-37_S81_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC31A-BGKcLV33-K562	brenton-graveley:SEC31A-BGKcLV33-38	brenton-graveley:L-SEC31A-BGKcLV33-38	brenton-graveley:SEC31A-BGKcLV33-38_S82_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC31A-BGKcLV33-38_S82_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR218ITU	ENCBS820TRC	ENCLB602NAY	ENCFF186PLZ	ENCFF393HYM	ENCSR848NDO	ENCBS258NMY	ENCLB714DBW	ENCFF654UKO	ENCFF619CGF
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	BGKcLV33-37	BGKcLV33-37	BGKcLV33-37	BGKcLV33-37	BGKcLV33-37	BGKcLV33-37	BGKcLV33-38	BGKcLV33-38	BGKcLV33-38	BGKcLV33-38
Sample Name	SEC31A-BGKcLV33-37	SEC31A-BGKcLV33-37	SEC31A-BGKcLV33-37	SEC31A-BGKcLV33-37	SEC31A-BGKcLV33-37	SEC31A-BGKcLV33-37	SEC31A-BGKcLV33-38	SEC31A-BGKcLV33-38	SEC31A-BGKcLV33-38	SEC31A-BGKcLV33-38
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		SEC31A-BGKcLV33-37.pdf	L-SEC31A-BGKcLV33-37.pdf				SEC31A-BGKcLV33-38.pdf	L-SEC31A-BGKcLV33-38.pdf
ID	7484	7577	7687	7797	7907	7973	7578	7688	7798	7908

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
SEC31A-BGKcLV33-37_S81_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2055	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	6633
SEC31A-BGKcLV33-37_S81_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2055	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	6689
SEC31A-BGKcLV33-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2055					GRCh38	V40	SEC31A-BGKcLV33-37_S81_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC31A-BGKcLV33-37_S81_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18110
SEC31A-BGKcLV33-37_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	2055					GRCh38	V40	SEC31A-BGKcLV33-37/Aligned.sortedByCoord.out.bam		ENCORE2	18166
SEC31A-BGKcLV33-37_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	2055					GRCh38	V40	SEC31A-BGKcLV33-37/Aligned.sortedByCoord.out.bam		ENCORE2	18222
SEC31A-BGKcLV33-37_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	2055					GRCh38	V40	SEC31A-BGKcLV33-37/Aligned.sortedByCoord.out.bam		ENCORE2	18278
SEC31A-BGKcLV33-37_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	2055					GRCh38	V40	SEC31A-BGKcLV33-37/Aligned.sortedByCoord.out.bam		ENCORE2	18334
SEC31A-BGKcLV33-37_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2055					GRCh38	V40	SEC31A-BGKcLV33-37_S81_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC31A-BGKcLV33-37_S81_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18390
SEC31A-BGKcLV33-38_S82_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2056	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	6634
SEC31A-BGKcLV33-38_S82_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2056	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	6690
SEC31A-BGKcLV33-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2056					GRCh38	V40	SEC31A-BGKcLV33-38_S82_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC31A-BGKcLV33-38_S82_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18111
SEC31A-BGKcLV33-38_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	2056					GRCh38	V40	SEC31A-BGKcLV33-38/Aligned.sortedByCoord.out.bam		ENCORE2	18167
SEC31A-BGKcLV33-38_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	2056					GRCh38	V40	SEC31A-BGKcLV33-38/Aligned.sortedByCoord.out.bam		ENCORE2	18223
SEC31A-BGKcLV33-38_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	2056					GRCh38	V40	SEC31A-BGKcLV33-38/Aligned.sortedByCoord.out.bam		ENCORE2	18279
SEC31A-BGKcLV33-38_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	2056					GRCh38	V40	SEC31A-BGKcLV33-38/Aligned.sortedByCoord.out.bam		ENCORE2	18335
SEC31A-BGKcLV33-38_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2056					GRCh38	V40	SEC31A-BGKcLV33-38_S82_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC31A-BGKcLV33-38_S82_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18391