SEPT7 RNA-Seq in K562

Experiment Information (Status: Released)

	BGKcLV33-41	BGKcLV33-41	BGKcLV33-42	BGKcLV33-42
idx	1143	1228	1144	1229
TRCN#_or_BGC#	BGC#0000860	BGC#0000853	BGC#0000860	BGC#0000853
shRNA_or_gRNA_sequence	AGGTTTTGAATTCACGCTTA	GATCACGATGAGCCCCACGA	AGGTTTTGAATTCACGCTTA	GATCACGATGAGCCCCACGA
PAM	TGG	AGG	TGG	AGG
Name	SEPTIN7_87	SEC63_94	SEPTIN7_87	SEC63_94
Sample_ID	BGKcLV33-41	BGKcLV33-41	BGKcLV33-42	BGKcLV33-42
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	SEPT7	SEC63	SEPT7	SEC63
qPCR_result		0.0		28.0
Ave_qPCR		14.0
RT-qPCR_primer-F		caacaaagcatacagcgaaaag
RT-qPCR_primer-R		tctgcaatgtaaagccacca
protein_conc	446	2596	469	2047
WB_result	0.0	76.6	0.0	67.8
Ave_WB	0.0	72.2
WB_DONE_date	1/24/22	3/10/22
MW	51kd	88kd
IP
antibody_Cat#	A304-212A	A305-084A	LOT #1	LOT #1
Antibody DCC ID		ENCAB877MEL		8/4/22
submitted_to_DCC_date
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	5283	5370	5284	5371

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SEC63	Product_ID: A305-084A Lot_ID: 1 Source: Bethyl Labs Target Name: SEC63-human

Experiment Status

	BGKcLV33-41	BGKcLV33-41	BGKcLV33-42	BGKcLV33-42
Sample_ID	BGKcLV33-41	BGKcLV33-41	BGKcLV33-42	BGKcLV33-42
Sample Name
Sample Name	SEC63-BGKcLV33-41		SEC63-BGKcLV33-42
RBP	SEC63	SEPT7	SEC63	SEPT7
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	10661	10727	10662	10728

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-41	BGKcLV33-42
Sample #	31	32
Sample Name	SEC63-BGKcLV33-41	SEC63-BGKcLV33-42
Sample_Name_Alias
Index Well Position	G04	H04
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	289
Peak_Molarity	60.50	64.10
libSampleQC_DNA_Well	DNA_Library_set53/set1/G8.png	DNA_Library_set53/set1/H8.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set53/set1/G4.png	RNA_Library_set53/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-41	BGKcLV33-42
RBP	SEC63	SEC63
Batch_ID	BGKcLV33	BGKcLV33
WB_result	76.600	67.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3292	3293

Sequencing Information

	BGKcLV33-41	BGKcLV33-42
Sample_ID	BGKcLV33-41	BGKcLV33-42
Sample Name	SEC63-BGKcLV33-41	SEC63-BGKcLV33-42
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	83,594,108	110,940,928
total_aligned_reads	74,205,298	97,305,554
unique_aligned_reads	67,823,518	88,826,054
percent_uniqueAligned	0.81134	0.80066
correlation_replicates	0.997723	0.997723
spikein_reads	2,380	11,238
percent_spikeins	0.00003	0.00010
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2059	2060

Data Submission Information

	BGKcLV33-41	BGKcLV33-41	BGKcLV33-41	BGKcLV33-41	BGKcLV33-41	BGKcLV33-41	BGKcLV33-42	BGKcLV33-42	BGKcLV33-42	BGKcLV33-42
ENCODE_alias	brenton-graveley:SEC63-BGKcLV33	brenton-graveley:SEC63-BGKcLV33-41	brenton-graveley:L-SEC63-BGKcLV33-41	brenton-graveley:SEC63-BGKcLV33-41_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC63-BGKcLV33-41_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC63-BGKcLV33-K562	brenton-graveley:SEC63-BGKcLV33-42	brenton-graveley:L-SEC63-BGKcLV33-42	brenton-graveley:SEC63-BGKcLV33-42_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC63-BGKcLV33-42_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR082BCP	ENCBS840KHA	ENCLB051KWA	ENCFF990SPS	ENCFF166IFE	ENCSR058HZP	ENCBS695AAR	ENCLB318NZC	ENCFF690FSN	ENCFF470VET
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	BGKcLV33-41	BGKcLV33-41	BGKcLV33-41	BGKcLV33-41	BGKcLV33-41	BGKcLV33-41	BGKcLV33-42	BGKcLV33-42	BGKcLV33-42	BGKcLV33-42
Sample Name	SEC63-BGKcLV33-41	SEC63-BGKcLV33-41	SEC63-BGKcLV33-41	SEC63-BGKcLV33-41	SEC63-BGKcLV33-41	SEC63-BGKcLV33-41	SEC63-BGKcLV33-42	SEC63-BGKcLV33-42	SEC63-BGKcLV33-42	SEC63-BGKcLV33-42
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		SEC63-BGKcLV33-41.pdf	L-SEC63-BGKcLV33-41.pdf				SEC63-BGKcLV33-42.pdf	L-SEC63-BGKcLV33-42.pdf
ID	7486	7581	7691	7801	7911	7975	7582	7692	7802	7912

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
SEC63-BGKcLV33-41_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2059	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	6637
SEC63-BGKcLV33-41_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2059	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	6693
SEC63-BGKcLV33-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2059					GRCh38	V40	SEC63-BGKcLV33-41_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC63-BGKcLV33-41_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18114
SEC63-BGKcLV33-41_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	2059					GRCh38	V40	SEC63-BGKcLV33-41/Aligned.sortedByCoord.out.bam		ENCORE2	18170
SEC63-BGKcLV33-41_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	2059					GRCh38	V40	SEC63-BGKcLV33-41/Aligned.sortedByCoord.out.bam		ENCORE2	18226
SEC63-BGKcLV33-41_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	2059					GRCh38	V40	SEC63-BGKcLV33-41/Aligned.sortedByCoord.out.bam		ENCORE2	18282
SEC63-BGKcLV33-41_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	2059					GRCh38	V40	SEC63-BGKcLV33-41/Aligned.sortedByCoord.out.bam		ENCORE2	18338
SEC63-BGKcLV33-41_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2059					GRCh38	V40	SEC63-BGKcLV33-41_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC63-BGKcLV33-41_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18394
SEC63-BGKcLV33-42_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2060	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	6638
SEC63-BGKcLV33-42_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2060	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	6694
SEC63-BGKcLV33-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2060					GRCh38	V40	SEC63-BGKcLV33-42_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC63-BGKcLV33-42_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18115
SEC63-BGKcLV33-42_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	2060					GRCh38	V40	SEC63-BGKcLV33-42/Aligned.sortedByCoord.out.bam		ENCORE2	18171
SEC63-BGKcLV33-42_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	2060					GRCh38	V40	SEC63-BGKcLV33-42/Aligned.sortedByCoord.out.bam		ENCORE2	18227
SEC63-BGKcLV33-42_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	2060					GRCh38	V40	SEC63-BGKcLV33-42/Aligned.sortedByCoord.out.bam		ENCORE2	18283
SEC63-BGKcLV33-42_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	2060					GRCh38	V40	SEC63-BGKcLV33-42/Aligned.sortedByCoord.out.bam		ENCORE2	18339
SEC63-BGKcLV33-42_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2060					GRCh38	V40	SEC63-BGKcLV33-42_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC63-BGKcLV33-42_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18395