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

General Information

List KD experiments controlled by BGRSLV07-1 and BGRSLV07-2

NT-BGRSLV07-1,NT-BGRSLV07-2:

ARIH1-BGRSLV07-RS293

LITAF-BGRSLV07-RS293

MCM10-BGRSLV07-RS293

REPIN1-BGRSLV07-RS293

RNF214-BGRSLV07-RS293

RNF31-BGRSLV07-RS293

TRIM2-BGRSLV07-RS293

ZCCHC10-BGRSLV07-RS293

ZNF214-BGRSLV07-RS293

ZNF346-BGRSLV07-RS293

Experiment Information (Status: Submitted)

	BGRSLV07-1	BGRSLV07-2
idx	0	0
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGRSLV07-1	BGRSLV07-2
transduction_Date	4/10/23	4/10/23
days	D4	D4
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
ID	8583	8584

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV07-1	BGRSLV07-2
Sample_ID	BGRSLV07-1	BGRSLV07-2
Sample Name
Sample Name	NT-BGRSLV07-1	NT-BGRSLV07-2
RBP	non-target	non-target
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	11836	11837

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV07-1	BGRSLV07-2
Sample #	17	18
Sample Name	NT-BGRSLV07-1	NT-BGRSLV07-2
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	284	297
Peak_Molarity	64.20	63.20
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/A3.png	DNA_Library_set60-62/set4/B3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/A3.png	RNA_Library_set60-62/set3/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV07-1	BGRSLV07-2
RBP	NT	NT
Batch_ID	BGRSLV07	BGRSLV07
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3700	3701

Sequencing Information

	BGRSLV07-1	BGRSLV07-2
Sample_ID	BGRSLV07-1	BGRSLV07-2
Sample Name	NT-BGRSLV07-1	NT-BGRSLV07-2
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	29,847,989	25,023,515
total_aligned_reads	21,030,636	20,474,309
unique_aligned_reads	19,653,452	19,177,792
percent_uniqueAligned	0.65845	0.76639
correlation_replicates	0.994236	0.994236
spikein_reads	91,712	46,558
percent_spikeins	0.00307	0.00186
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2571	2572

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-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2571	NovaSeq6000	100	paired-ended	1				ENCORE2	7880
NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2571	NovaSeq6000	100	paired-ended	2				ENCORE2	7924
NT-BGRSLV07-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2571					GRCh38	V40	NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10185
NT-BGRSLV07-1_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2571					GRCh38	V40	NT-BGRSLV07-1/Aligned.sortedByCoord.out.bam	ENCORE2	10229
NT-BGRSLV07-1_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2571					GRCh38	V40	NT-BGRSLV07-1/Aligned.sortedByCoord.out.bam	ENCORE2	10273
NT-BGRSLV07-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2571					GRCh38	V40	NT-BGRSLV07-1/Aligned.sortedByCoord.out.bam	ENCORE2	10317
NT-BGRSLV07-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2571					GRCh38	V40	NT-BGRSLV07-1/Aligned.sortedByCoord.out.bam	ENCORE2	10361
NT-BGRSLV07-1_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2571					GRCh38	V40	NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10405
NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2572	NovaSeq6000	100	paired-ended	1				ENCORE2	7881
NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2572	NovaSeq6000	100	paired-ended	2				ENCORE2	7925
NT-BGRSLV07-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2572					GRCh38	V40	NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10186
NT-BGRSLV07-2_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2572					GRCh38	V40	NT-BGRSLV07-2/Aligned.sortedByCoord.out.bam	ENCORE2	10230
NT-BGRSLV07-2_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2572					GRCh38	V40	NT-BGRSLV07-2/Aligned.sortedByCoord.out.bam	ENCORE2	10274
NT-BGRSLV07-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2572					GRCh38	V40	NT-BGRSLV07-2/Aligned.sortedByCoord.out.bam	ENCORE2	10318
NT-BGRSLV07-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2572					GRCh38	V40	NT-BGRSLV07-2/Aligned.sortedByCoord.out.bam	ENCORE2	10362
NT-BGRSLV07-2_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2572					GRCh38	V40	NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10406