non-target RNA-Seq in Ribo-STAMP-293T

General Information

List KD experiments controlled by BGRSDTLV02-3doxtot and BGRSDTLV02-4doxtot

NT-BGRSDTLV02-3doxtot,NT-BGRSDTLV02-4doxtot:

Experiment Information (Status: Submitted)

	BGRSDTLV02-3doxtot	BGRSDTLV02-4doxtot
idx	0	0
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGRSDTLV02-3doxtot	BGRSDTLV02-4doxtot
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
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	sample experiment in BGRSDLV02, Total-RNA	sample experiment in BGRSDLV02, Total-RNA
ID	9308	9309

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDTLV02-3doxtot	BGRSDTLV02-4doxtot
Sample_ID	BGRSDTLV02-3doxtot	BGRSDTLV02-4doxtot
Sample Name
Sample Name	NT-BGRSDTLV02-3doxtot	NT-BGRSDTLV02-4doxtot
RBP	non-target	non-target
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12414	12415

Library-Prep
Sequencing

Library-Prep Information

	BGRSDTLV02-3doxtot	BGRSDTLV02-4doxtot
Sample #	79	80
Sample Name	NT-BGRSDTLV02-3doxtot	NT-BGRSDTLV02-4doxtot
Sample_Name_Alias
Index Well Position	C11	D11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-27	2023-09-27
Lib_ID	Lib-230927	Lib-230927
Tecan_Location
Tecan
Tecan_date
Size_bp	268	271
Peak_Molarity	4.45	39.90
libSampleQC_DNA_Well	DNA_Library_set65_tot/set1/C11.png	DNA_Library_set65_tot/set1/D11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/C1.png	RNA_Library_set65/set1/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-03	2023-10-03
Sample_ID	BGRSDTLV02-3doxtot	BGRSDTLV02-4doxtot
RBP	NT	NT
Batch_ID	BGRSDTLV02	BGRSDTLV02
WB_result	0.000	0.000
Library Description	TruSeq Total RNA	TruSeq Total RNA
Repeat_Library_Suffix	t	t
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4000	4001

Sequencing Information

	BGRSDTLV02-3doxtot	BGRSDTLV02-4doxtot
Sample_ID	BGRSDTLV02-3doxtot	BGRSDTLV02-4doxtot
Sample Name	NT-BGRSDTLV02-3doxtot	NT-BGRSDTLV02-4doxtot
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65_tot	set65_tot
total_reads	52,825,350	39,495,749
total_aligned_reads	37,408,499	34,035,705
unique_aligned_reads	33,997,629	30,689,468
percent_uniqueAligned	0.64359	0.77703
correlation_replicates	0.980095	0.980095
spikein_reads	209,964	100,030
percent_spikeins	0.00397	0.00253
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2747	2748

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	Project	FILE_ID
NT-BGRSDTLV02-3doxtot_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2747	NovaSeq6000	100	paired-ended	1				ENCORE2	8892
NT-BGRSDTLV02-3doxtot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2747	NovaSeq6000	100	paired-ended	2				ENCORE2	8900
NT-BGRSDTLV02-3doxtot_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2747					GRCh38	V40	NT-BGRSDTLV02-3doxtot_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-3doxtot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9257
NT-BGRSDTLV02-3doxtot_Signal.Unique.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2747					GRCh38	V40	NT-BGRSDTLV02-3doxtot/Aligned.sortedByCoord.out.bam	ENCORE2	9265
NT-BGRSDTLV02-3doxtot_Signal.Unique.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2747					GRCh38	V40	NT-BGRSDTLV02-3doxtot/Aligned.sortedByCoord.out.bam	ENCORE2	9273
NT-BGRSDTLV02-3doxtot_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2747					GRCh38	V40	NT-BGRSDTLV02-3doxtot/Aligned.sortedByCoord.out.bam	ENCORE2	9281
NT-BGRSDTLV02-3doxtot_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2747					GRCh38	V40	NT-BGRSDTLV02-3doxtot/Aligned.sortedByCoord.out.bam	ENCORE2	9289
NT-BGRSDTLV02-3doxtot_quant.sf	ENCODE_DATA/set65_tot/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2747					GRCh38	V40	NT-BGRSDTLV02-3doxtot_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-3doxtot_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9297
NT-BGRSDTLV02-4doxtot_S80_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2748	NovaSeq6000	100	paired-ended	1				ENCORE2	8893
NT-BGRSDTLV02-4doxtot_S80_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65_tot/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2748	NovaSeq6000	100	paired-ended	2				ENCORE2	8901
NT-BGRSDTLV02-4doxtot_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2748					GRCh38	V40	NT-BGRSDTLV02-4doxtot_S80_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-4doxtot_S80_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9258
NT-BGRSDTLV02-4doxtot_Signal.Unique.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2748					GRCh38	V40	NT-BGRSDTLV02-4doxtot/Aligned.sortedByCoord.out.bam	ENCORE2	9266
NT-BGRSDTLV02-4doxtot_Signal.Unique.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2748					GRCh38	V40	NT-BGRSDTLV02-4doxtot/Aligned.sortedByCoord.out.bam	ENCORE2	9274
NT-BGRSDTLV02-4doxtot_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2748					GRCh38	V40	NT-BGRSDTLV02-4doxtot/Aligned.sortedByCoord.out.bam	ENCORE2	9282
NT-BGRSDTLV02-4doxtot_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65_tot/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2748					GRCh38	V40	NT-BGRSDTLV02-4doxtot/Aligned.sortedByCoord.out.bam	ENCORE2	9290
NT-BGRSDTLV02-4doxtot_quant.sf	ENCODE_DATA/set65_tot/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2748					GRCh38	V40	NT-BGRSDTLV02-4doxtot_S80_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDTLV02-4doxtot_S80_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	9298