SEC63 RNA-Seq in HepG2

General Information


RBP	SEC63
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SEC63-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR420PTK
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR981TQN
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	SEC63-BGHcLV31-37
Rep2	SEC63-BGHcLV31-38
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR	32.8
Rep2_qPCR	26.1
Rep1_WB	50.9
Rep2_WB	51.0
Antibody Cat#	A305-084A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB877MEL
Status	Submitted
Project	ENCODE4
ID	929

Experiment Information (Status: Released)

	BGHcLV31-37	BGHcLV31-38
idx	957	958
TRCN#_or_BGC#	BGC#0000853	BGC#0000853
shRNA_or_gRNA_sequence	GATCACGATGAGCCCCACGA	GATCACGATGAGCCCCACGA
PAM	AGG	AGG
Name	SEC63_94	SEC63_94
Sample_ID	BGHcLV31-37	BGHcLV31-38
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	SEC63	SEC63
qPCR_result	32.8	26.1
Ave_qPCR	29.5
RT-qPCR_primer-F	caacaaagcatacagcgaaaag
RT-qPCR_primer-R	tctgcaatgtaaagccacca
protein_conc	4455	4808
WB_result	50.9	51.0
Ave_WB	50.9
WB_DONE_date	11/8/21
MW	88kd
IP
antibody_Cat#	A305-084A	LOT #1
Antibody DCC ID	ENCAB877MEL
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/16/21	12/16/21
repeat_library
Note
ID	7136	7137

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

	BGHcLV31-37	BGHcLV31-38
Sample_ID	BGHcLV31-37	BGHcLV31-38
Sample Name
Sample Name	SEC63-BGHcLV31-37	SEC63-BGHcLV31-38
RBP	SEC63	SEC63
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10313	10314

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-37	BGHcLV31-38
Sample #	27	28
Sample Name	SEC63-BGHcLV31-37	SEC63-BGHcLV31-38
Sample_Name_Alias
Index Well Position	C04	D04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-12-16	2021-12-16
Lib_ID	Lib-211216	Lib-211216
Tecan_Location
Tecan
Tecan_date
Size_bp	294	288
Peak_Molarity	62.90	75.80
libSampleQC_DNA_Well	DNA_Library_set52/set1/C11.png	DNA_Library_set52/set1/D11.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set52/set1/C4.png	RNA_Library_set52/set1/D4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-37	BGHcLV31-38
RBP	SEC63	SEC63
Batch_ID	BGHcLV31	BGHcLV31
WB_result	50.900	51.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3204	3205

Sequencing Information

	BGHcLV31-37	BGHcLV31-38
Sample_ID	BGHcLV31-37	BGHcLV31-38
Sample Name	SEC63-BGHcLV31-37	SEC63-BGHcLV31-38
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	104,057,292	106,765,282
total_aligned_reads	93,817,064	95,000,266
unique_aligned_reads	88,614,592	89,461,180
percent_uniqueAligned	0.85159	0.83792
correlation_replicates	0.982613	0.982613
spikein_reads	5,206	2,996
percent_spikeins	0.00005	0.00003
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2001	2002

Data Submission Information

	BGHcLV31-37	BGHcLV31-37	BGHcLV31-37	BGHcLV31-37	BGHcLV31-37	BGHcLV31-37	BGHcLV31-38	BGHcLV31-38	BGHcLV31-38	BGHcLV31-38
ENCODE_alias	brenton-graveley:SEC63-BGHcLV31	brenton-graveley:SEC63-BGHcLV31-37	brenton-graveley:L-SEC63-BGHcLV31-37	brenton-graveley:SEC63-BGHcLV31-37_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC63-BGHcLV31-37_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC63-BGHcLV31-HepG2	brenton-graveley:SEC63-BGHcLV31-38	brenton-graveley:L-SEC63-BGHcLV31-38	brenton-graveley:SEC63-BGHcLV31-38_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC63-BGHcLV31-38_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR981TQN	ENCBS920CHH	ENCLB368SBH	ENCFF599CIQ	ENCFF790LGZ	ENCSR420PTK	ENCBS451EGX	ENCLB349MUK	ENCFF351XME	ENCFF014ENF
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	BGHcLV31-37	BGHcLV31-37	BGHcLV31-37	BGHcLV31-37	BGHcLV31-37	BGHcLV31-37	BGHcLV31-38	BGHcLV31-38	BGHcLV31-38	BGHcLV31-38
Sample Name	SEC63-BGHcLV31-37	SEC63-BGHcLV31-37	SEC63-BGHcLV31-37	SEC63-BGHcLV31-37	SEC63-BGHcLV31-37	SEC63-BGHcLV31-37	SEC63-BGHcLV31-38	SEC63-BGHcLV31-38	SEC63-BGHcLV31-38	SEC63-BGHcLV31-38
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
		LV52_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		SEC63-BGHcLV31-37.pdf	L-SEC63-BGHcLV31-37.pdf				SEC63-BGHcLV31-38.pdf	L-SEC63-BGHcLV31-38.pdf
ID	7457	7525	7633	7743	7853	7949	7526	7634	7744	7854

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-BGHcLV31-37_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2001	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6547
SEC63-BGHcLV31-37_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2001	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6601
SEC63-BGHcLV31-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2001					GRCh38	V40	SEC63-BGHcLV31-37_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC63-BGHcLV31-37_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18468
SEC63-BGHcLV31-37_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2001					GRCh38	V40	SEC63-BGHcLV31-37/Aligned.sortedByCoord.out.bam		ENCORE2	18522
SEC63-BGHcLV31-37_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2001					GRCh38	V40	SEC63-BGHcLV31-37/Aligned.sortedByCoord.out.bam		ENCORE2	18576
SEC63-BGHcLV31-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2001					GRCh38	V40	SEC63-BGHcLV31-37/Aligned.sortedByCoord.out.bam		ENCORE2	18630
SEC63-BGHcLV31-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2001					GRCh38	V40	SEC63-BGHcLV31-37/Aligned.sortedByCoord.out.bam		ENCORE2	18684
SEC63-BGHcLV31-37_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2001					GRCh38	V40	SEC63-BGHcLV31-37_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC63-BGHcLV31-37_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18738
SEC63-BGHcLV31-38_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2002	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6548
SEC63-BGHcLV31-38_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2002	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6602
SEC63-BGHcLV31-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2002					GRCh38	V40	SEC63-BGHcLV31-38_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC63-BGHcLV31-38_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18469
SEC63-BGHcLV31-38_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2002					GRCh38	V40	SEC63-BGHcLV31-38/Aligned.sortedByCoord.out.bam		ENCORE2	18523
SEC63-BGHcLV31-38_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2002					GRCh38	V40	SEC63-BGHcLV31-38/Aligned.sortedByCoord.out.bam		ENCORE2	18577
SEC63-BGHcLV31-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2002					GRCh38	V40	SEC63-BGHcLV31-38/Aligned.sortedByCoord.out.bam		ENCORE2	18631
SEC63-BGHcLV31-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2002					GRCh38	V40	SEC63-BGHcLV31-38/Aligned.sortedByCoord.out.bam		ENCORE2	18685
SEC63-BGHcLV31-38_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2002					GRCh38	V40	SEC63-BGHcLV31-38_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC63-BGHcLV31-38_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18739