SEC62 RNA-Seq in HepG2

General Information


RBP	SEC62
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SEC62-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR586DOD
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR094AES
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	SEC62-BGHcLV31-35
Rep2	SEC62-BGHcLV31-36
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR	40.5
Rep2_qPCR	41.5
Rep1_WB	67.6
Rep2_WB	58.8
Antibody Cat#	A303-981A
Antibody Lot#	LOT #1
Antibody DCC ID
Status	Submitted
Project	ENCODE4
ID	928

Experiment Information (Status: Released)

	BGHcLV31-35	BGHcLV31-36
idx	955	956
TRCN#_or_BGC#	BGC#0000851	BGC#0000851
shRNA_or_gRNA_sequence	CCACCAATATGATGGGTCAC	CCACCAATATGATGGGTCAC
PAM	CGG	CGG
Name	SEC62_84	SEC62_84
Sample_ID	BGHcLV31-35	BGHcLV31-36
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	SEC62	SEC62
qPCR_result	40.5	41.5
Ave_qPCR	41.0
RT-qPCR_primer-F	gaaggctgtggccaagtatc
RT-qPCR_primer-R	cctctcctttcttggccttt
protein_conc	4385	3549
WB_result	67.6	58.8
Ave_WB	63.2
WB_DONE_date	11/8/21
MW	46kd
IP
antibody_Cat#	A303-981A	LOT #1
Antibody DCC ID
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	7134	7135

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV31-35	BGHcLV31-36
Sample_ID	BGHcLV31-35	BGHcLV31-36
Sample Name
Sample Name	SEC62-BGHcLV31-35	SEC62-BGHcLV31-36
RBP	SEC62	SEC62
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10311	10312

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-35	BGHcLV31-36
Sample #	25	26
Sample Name	SEC62-BGHcLV31-35	SEC62-BGHcLV31-36
Sample_Name_Alias
Index Well Position	A04	B04
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	293	293
Peak_Molarity	63.10	62.20
libSampleQC_DNA_Well	DNA_Library_set52/set1/A11.png	DNA_Library_set52/set1/B11.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set52/set1/A4.png	RNA_Library_set52/set1/B4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-35	BGHcLV31-36
RBP	SEC62	SEC62
Batch_ID	BGHcLV31	BGHcLV31
WB_result	67.600	58.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3202	3203

Sequencing Information

	BGHcLV31-35	BGHcLV31-36
Sample_ID	BGHcLV31-35	BGHcLV31-36
Sample Name	SEC62-BGHcLV31-35	SEC62-BGHcLV31-36
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	87,034,940	81,421,380
total_aligned_reads	79,218,790	72,131,042
unique_aligned_reads	74,690,884	68,024,632
percent_uniqueAligned	0.85817	0.83546
correlation_replicates	0.993992	0.993992
spikein_reads	7,910	6,458
percent_spikeins	0.00009	0.00008
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1999	2000

Data Submission Information

	BGHcLV31-35	BGHcLV31-35	BGHcLV31-35	BGHcLV31-35	BGHcLV31-35	BGHcLV31-35	BGHcLV31-36	BGHcLV31-36	BGHcLV31-36	BGHcLV31-36
ENCODE_alias	brenton-graveley:SEC62-BGHcLV31	brenton-graveley:SEC62-BGHcLV31-35	brenton-graveley:L-SEC62-BGHcLV31-35	brenton-graveley:SEC62-BGHcLV31-35_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC62-BGHcLV31-35_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC62-BGHcLV31-HepG2	brenton-graveley:SEC62-BGHcLV31-36	brenton-graveley:L-SEC62-BGHcLV31-36	brenton-graveley:SEC62-BGHcLV31-36_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SEC62-BGHcLV31-36_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR094AES	ENCBS391QCN	ENCLB645XAR	ENCFF335FHB	ENCFF798PDZ	ENCSR586DOD	ENCBS029UTH	ENCLB616DSP	ENCFF514VXN	ENCFF982LZB
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	BGHcLV31-35	BGHcLV31-35	BGHcLV31-35	BGHcLV31-35	BGHcLV31-35	BGHcLV31-35	BGHcLV31-36	BGHcLV31-36	BGHcLV31-36	BGHcLV31-36
Sample Name	SEC62-BGHcLV31-35	SEC62-BGHcLV31-35	SEC62-BGHcLV31-35	SEC62-BGHcLV31-35	SEC62-BGHcLV31-35	SEC62-BGHcLV31-35	SEC62-BGHcLV31-36	SEC62-BGHcLV31-36	SEC62-BGHcLV31-36	SEC62-BGHcLV31-36
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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_library_protocol					LV52_library_protocol
protocol_URL			L-SEC62-BGHcLV31-35.pdf					L-SEC62-BGHcLV31-36.pdf
ID	7456	7523	7631	7741	7851	7948	7524	7632	7742	7852

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
SEC62-BGHcLV31-35_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1999	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	6545
SEC62-BGHcLV31-35_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1999	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	6599
SEC62-BGHcLV31-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1999					GRCh38	V40	SEC62-BGHcLV31-35_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC62-BGHcLV31-35_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18466
SEC62-BGHcLV31-35_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	1999					GRCh38	V40	SEC62-BGHcLV31-35/Aligned.sortedByCoord.out.bam		ENCORE2	18520
SEC62-BGHcLV31-35_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	1999					GRCh38	V40	SEC62-BGHcLV31-35/Aligned.sortedByCoord.out.bam		ENCORE2	18574
SEC62-BGHcLV31-35_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	1999					GRCh38	V40	SEC62-BGHcLV31-35/Aligned.sortedByCoord.out.bam		ENCORE2	18628
SEC62-BGHcLV31-35_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	1999					GRCh38	V40	SEC62-BGHcLV31-35/Aligned.sortedByCoord.out.bam		ENCORE2	18682
SEC62-BGHcLV31-35_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1999					GRCh38	V40	SEC62-BGHcLV31-35_S25_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC62-BGHcLV31-35_S25_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18736
SEC62-BGHcLV31-36_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2000	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	6546
SEC62-BGHcLV31-36_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2000	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	6600
SEC62-BGHcLV31-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2000					GRCh38	V40	SEC62-BGHcLV31-36_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC62-BGHcLV31-36_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18467
SEC62-BGHcLV31-36_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	2000					GRCh38	V40	SEC62-BGHcLV31-36/Aligned.sortedByCoord.out.bam		ENCORE2	18521
SEC62-BGHcLV31-36_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	2000					GRCh38	V40	SEC62-BGHcLV31-36/Aligned.sortedByCoord.out.bam		ENCORE2	18575
SEC62-BGHcLV31-36_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	2000					GRCh38	V40	SEC62-BGHcLV31-36/Aligned.sortedByCoord.out.bam		ENCORE2	18629
SEC62-BGHcLV31-36_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	2000					GRCh38	V40	SEC62-BGHcLV31-36/Aligned.sortedByCoord.out.bam		ENCORE2	18683
SEC62-BGHcLV31-36_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2000					GRCh38	V40	SEC62-BGHcLV31-36_S26_L001_R1_001.filtered.trimmed.paired.fastq.gz,SEC62-BGHcLV31-36_S26_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18737