SEC23IP RNA-Seq in HepG2

General Information


RBP	SEC23IP
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SEC23IP-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR010WDI
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR745KNE
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	SEC23IP-BGHcLV31-31
Rep2	SEC23IP-BGHcLV31-32
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR	32.6
Rep2_qPCR	39.5
Rep1_WB	87.1
Rep2_WB	87.6
Antibody Cat#	A300-592A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB911OUO
Status	Submitted
Project	ENCODE4
ID	927

Experiment Information (Status: Released)

	BGHcLV31-31	BGHcLV31-31	BGHcLV31-32	BGHcLV31-32
idx	949	951	950	952
TRCN#_or_BGC#	BGC#0000848	BGC#0000848	BGC#0000848	BGC#0000848
shRNA_or_gRNA_sequence	GCCGAGAGAAAACCTAACGG	GCCGAGAGAAAACCTAACGG	GCCGAGAGAAAACCTAACGG	GCCGAGAGAAAACCTAACGG
PAM	TGG	TGG	TGG	TGG
Name	SEC23IP_96	SEC23IP_96	SEC23IP_96	SEC23IP_96
Sample_ID	BGHcLV31-31	BGHcLV31-31	BGHcLV31-32	BGHcLV31-32
transduction_Date	9/23/21	9/23/21	9/23/21	9/23/21
days	D6	D6	D6	D6
RBP_name	SEC23IP	SEC23IP	SEC23IP	SEC23IP
qPCR_result	32.6	32.6	39.5	39.5
Ave_qPCR	36.1	36.1
RT-qPCR_primer-F	tcctcagtgccagatgaatg	tcctcagtgccagatgaatg
RT-qPCR_primer-R	ccacaaacaccaaatggtca	ccacaaacaccaaatggtca
protein_conc	4453	4453	4552	4552
WB_result	87.1	94.2	87.6	87.0
Ave_WB	87.4	90.6
WB_DONE_date	11/10/21	4/18/22
MW	111kd	111kd
IP
antibody_Cat#	A300-592A	A300-594A	LOT #1	LOT #1
Antibody DCC ID	ENCAB911OUO	ENCAB820MEZ
submitted_to_DCC_date
Rep1_TPM	21	0	0	0
Rep2_TPM	36	0	0	0
Action	Ready		Ready
Library_start_date	12/16/21		12/16/21
repeat_library
Note
ID	7128	7130	7129	7131

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SEC23IP	Product_ID: A300-592A Lot_ID: 1 Source: Bethyl Labs Target Name: SEC23IP-human
SEC23IP	Product_ID: A300-594A Lot_ID: 1 Source: Bethyl Labs Target Name: SEC23IP-human

Experiment Status

	BGHcLV31-31	BGHcLV31-32
Sample_ID	BGHcLV31-31	BGHcLV31-32
Sample Name
Sample Name	SEC23IP-BGHcLV31-31	SEC23IP-BGHcLV31-32
RBP	SEC23IP	SEC23IP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10309	10310

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-31	BGHcLV31-32
Sample #	23	24
Sample Name	SEC23IP-BGHcLV31-31	SEC23IP-BGHcLV31-32
Sample_Name_Alias
Index Well Position	G03	H03
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	286	286
Peak_Molarity	69.80	52.60
libSampleQC_DNA_Well	DNA_Library_set52/set1/G10.png	DNA_Library_set52/set1/H10.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_set52/set1/G3.png	RNA_Library_set52/set1/H3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-31	BGHcLV31-32
RBP	SEC23IP	SEC23IP
Batch_ID	BGHcLV31	BGHcLV31
WB_result	87.100	87.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3200	3201

Sequencing Information

	BGHcLV31-31	BGHcLV31-32
Sample_ID	BGHcLV31-31	BGHcLV31-32
Sample Name	SEC23IP-BGHcLV31-31	SEC23IP-BGHcLV31-32
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	113,911,924	109,498,694
total_aligned_reads	103,442,366	98,310,000
unique_aligned_reads	97,355,852	92,630,370
percent_uniqueAligned	0.85466	0.84595
correlation_replicates	0.997388	0.997388
spikein_reads	6,934	5,204
percent_spikeins	0.00006	0.00005
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1997	1998

Data Submission Information

	BGHcLV31-31	BGHcLV31-31	BGHcLV31-31	BGHcLV31-31	BGHcLV31-31	BGHcLV31-31	BGHcLV31-32	BGHcLV31-32	BGHcLV31-32	BGHcLV31-32
ENCODE_alias	brenton-graveley:SEC23IP-BGHcLV31	brenton-graveley:SEC23IP-BGHcLV31-31	brenton-graveley:L-SEC23IP-BGHcLV31-31	brenton-graveley:SEC23IP-BGHcLV31-31_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC23IP-BGHcLV31-31_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC23IP-BGHcLV31-HepG2	brenton-graveley:SEC23IP-BGHcLV31-32	brenton-graveley:L-SEC23IP-BGHcLV31-32	brenton-graveley:SEC23IP-BGHcLV31-32_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC23IP-BGHcLV31-32_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR745KNE	ENCBS023BGM	ENCLB873RFS	ENCFF810ZQD	ENCFF201NWK	ENCSR010WDI	ENCBS547LXE	ENCLB872BZK	ENCFF597RWS	ENCFF151NIT
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	BGHcLV31-31	BGHcLV31-31	BGHcLV31-31	BGHcLV31-31	BGHcLV31-31	BGHcLV31-31	BGHcLV31-32	BGHcLV31-32	BGHcLV31-32	BGHcLV31-32
Sample Name	SEC23IP-BGHcLV31-31	SEC23IP-BGHcLV31-31	SEC23IP-BGHcLV31-31	SEC23IP-BGHcLV31-31	SEC23IP-BGHcLV31-31	SEC23IP-BGHcLV31-31	SEC23IP-BGHcLV31-32	SEC23IP-BGHcLV31-32	SEC23IP-BGHcLV31-32	SEC23IP-BGHcLV31-32
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		SEC23IP-BGHcLV31-31.pdf	L-SEC23IP-BGHcLV31-31.pdf				SEC23IP-BGHcLV31-32.pdf	L-SEC23IP-BGHcLV31-32.pdf
ID	7455	7521	7629	7739	7849	7947	7522	7630	7740	7850

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
SEC23IP-BGHcLV31-31_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1997	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	6543
SEC23IP-BGHcLV31-31_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1997	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	6597
SEC23IP-BGHcLV31-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1997					GRCh38	V40	SEC23IP-BGHcLV31-31_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC23IP-BGHcLV31-31_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18464
SEC23IP-BGHcLV31-31_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	1997					GRCh38	V40	SEC23IP-BGHcLV31-31/Aligned.sortedByCoord.out.bam		ENCORE2	18518
SEC23IP-BGHcLV31-31_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	1997					GRCh38	V40	SEC23IP-BGHcLV31-31/Aligned.sortedByCoord.out.bam		ENCORE2	18572
SEC23IP-BGHcLV31-31_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	1997					GRCh38	V40	SEC23IP-BGHcLV31-31/Aligned.sortedByCoord.out.bam		ENCORE2	18626
SEC23IP-BGHcLV31-31_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	1997					GRCh38	V40	SEC23IP-BGHcLV31-31/Aligned.sortedByCoord.out.bam		ENCORE2	18680
SEC23IP-BGHcLV31-31_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1997					GRCh38	V40	SEC23IP-BGHcLV31-31_S23_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC23IP-BGHcLV31-31_S23_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18734
SEC23IP-BGHcLV31-32_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1998	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	6544
SEC23IP-BGHcLV31-32_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1998	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	6598
SEC23IP-BGHcLV31-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1998					GRCh38	V40	SEC23IP-BGHcLV31-32_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC23IP-BGHcLV31-32_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18465
SEC23IP-BGHcLV31-32_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	1998					GRCh38	V40	SEC23IP-BGHcLV31-32/Aligned.sortedByCoord.out.bam		ENCORE2	18519
SEC23IP-BGHcLV31-32_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	1998					GRCh38	V40	SEC23IP-BGHcLV31-32/Aligned.sortedByCoord.out.bam		ENCORE2	18573
SEC23IP-BGHcLV31-32_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	1998					GRCh38	V40	SEC23IP-BGHcLV31-32/Aligned.sortedByCoord.out.bam		ENCORE2	18627
SEC23IP-BGHcLV31-32_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	1998					GRCh38	V40	SEC23IP-BGHcLV31-32/Aligned.sortedByCoord.out.bam		ENCORE2	18681
SEC23IP-BGHcLV31-32_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1998					GRCh38	V40	SEC23IP-BGHcLV31-32_S24_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC23IP-BGHcLV31-32_S24_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18735