SEC23B RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV06-37	BGRSLV06-38
idx	0	0
TRCN#_or_BGC#	TRCN0000380710	TRCN0000380710
shRNA_or_gRNA_sequence	GTACCGGTGGTGCTACTTTGGACGTAAACTCGAGTTTACGTCCAAAGTAGCACCATTTTTTG	GTACCGGTGGTGCTACTTTGGACGTAAACTCGAGTTTACGTCCAAAGTAGCACCATTTTTTG
PAM
Name	SEC23B	SEC23B
Sample_ID	BGRSLV06-37	BGRSLV06-38
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	SEC23B	SEC23B
qPCR_result	74.8	75.0
Ave_qPCR	74.9
RT-qPCR_primer-F	gcattatcagcactccagca
RT-qPCR_primer-R	tgtgcctgagctgactctgt
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	8564	8565

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-37	BGRSLV06-38
Sample_ID	BGRSLV06-37	BGRSLV06-38
Sample Name
Sample Name	SEC23B-BGRSLV06-37	SEC23B-BGRSLV06-38
RBP	SEC23B	SEC23B
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11704	11705

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-37	BGRSLV06-38
Sample #	87	88
Sample Name	SEC23B-BGRSLV06-37	SEC23B-BGRSLV06-38
Sample_Name_Alias
Index Well Position	G11	H11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412B	Lib-230412B
Tecan_Location
Tecan
Tecan_date
Size_bp	303	315
Peak_Molarity	102.00	93.30
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/C12.png	DNA_Library_set60-62/set1/D12.png
RIN	9.4	9.1
libSample_RNA_Well	RNA_Library_set60-62/set1/G11.png	RNA_Library_set60-62/set1/H11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-37	BGRSLV06-38
RBP	SEC23B	SEC23B
Batch_ID	BGRSLV06	BGRSLV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3674	3675

Sequencing Information

	BGRSLV06-37	BGRSLV06-38
Sample_ID	BGRSLV06-37	BGRSLV06-38
Sample Name	SEC23B-BGRSLV06-37	SEC23B-BGRSLV06-38
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	28,350,505	46,905,480
total_aligned_reads	25,690,940	35,529,261
unique_aligned_reads	24,204,948	33,502,595
percent_uniqueAligned	0.85377	0.71426
correlation_replicates	0.986741	0.986741
spikein_reads	42,616	29,480
percent_spikeins	0.00150	0.00063
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2545	2546

Data Submission Information DCC submission information was not avaliable

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
SEC23B-BGRSLV06-37_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2545	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8602
SEC23B-BGRSLV06-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2545					GRCh38	V40	SEC23B-BGRSLV06-37_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC23B-BGRSLV06-37_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10467
SEC23B-BGRSLV06-37_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2545					GRCh38	V40	SEC23B-BGRSLV06-37/Aligned.sortedByCoord.out.bam		ENCORE2	10519
SEC23B-BGRSLV06-37_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2545					GRCh38	V40	SEC23B-BGRSLV06-37/Aligned.sortedByCoord.out.bam		ENCORE2	10571
SEC23B-BGRSLV06-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2545					GRCh38	V40	SEC23B-BGRSLV06-37/Aligned.sortedByCoord.out.bam		ENCORE2	10623
SEC23B-BGRSLV06-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2545					GRCh38	V40	SEC23B-BGRSLV06-37/Aligned.sortedByCoord.out.bam		ENCORE2	10675
SEC23B-BGRSLV06-37_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2545					GRCh38	V40	SEC23B-BGRSLV06-37_S87_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC23B-BGRSLV06-37_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10727
SEC23B-BGRSLV06-37_S87_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2545	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28869
SEC23B-BGRSLV06-38_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2546	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8603
SEC23B-BGRSLV06-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2546					GRCh38	V40	SEC23B-BGRSLV06-38_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC23B-BGRSLV06-38_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10468
SEC23B-BGRSLV06-38_Signal.Unique.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2546					GRCh38	V40	SEC23B-BGRSLV06-38/Aligned.sortedByCoord.out.bam		ENCORE2	10520
SEC23B-BGRSLV06-38_Signal.Unique.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2546					GRCh38	V40	SEC23B-BGRSLV06-38/Aligned.sortedByCoord.out.bam		ENCORE2	10572
SEC23B-BGRSLV06-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2546					GRCh38	V40	SEC23B-BGRSLV06-38/Aligned.sortedByCoord.out.bam		ENCORE2	10624
SEC23B-BGRSLV06-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2546					GRCh38	V40	SEC23B-BGRSLV06-38/Aligned.sortedByCoord.out.bam		ENCORE2	10676
SEC23B-BGRSLV06-38_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2546					GRCh38	V40	SEC23B-BGRSLV06-38_S88_L002_R1_001.filtered.trimmed.paired.fastq.gz,SEC23B-BGRSLV06-38_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10728
SEC23B-BGRSLV06-38_S88_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2546	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28870