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

General Information

List KD experiments controlled by BGRSLV06-1 and BGRSLV06-2

NT-BGRSLV06-1,NT-BGRSLV06-2:

MBNL2-BGRSLV06-RS293

RNF113A-BGRSLV06-RS293

RNF26-BGRSLV06-RS293

RNF43-BGRSLV06-RS293

RYBP-BGRSLV06-RS293

SEC23B-BGRSLV06-RS293

TRIM28-BGRSLV06-RS293

TUT1-BGRSLV06-RS293

ZNF16-BGRSLV06-RS293

ZNF169-BGRSLV06-RS293

Experiment Information (Status: Submitted)

	BGRSLV06-1	BGRSLV06-2
idx	0	0
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGRSLV06-1	BGRSLV06-2
transduction_Date	3/27/23	3/27/23
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	8528	8529

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-1	BGRSLV06-2
Sample_ID	BGRSLV06-1	BGRSLV06-2
Sample Name
Sample Name	NT-BGRSLV06-1	NT-BGRSLV06-2
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	11684	11685

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-1	BGRSLV06-2
Sample #	67	68
Sample Name	NT-BGRSLV06-1	NT-BGRSLV06-2
Sample_Name_Alias
Index Well Position	C09	D09
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	284	289
Peak_Molarity	129.00	60.70
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/G9.png	DNA_Library_set60-62/set1/H9.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set60-62/set1/C9.png	RNA_Library_set60-62/set1/D9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-1	BGRSLV06-2
RBP	NT	NT
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	3654	3655

Sequencing Information

	BGRSLV06-1	BGRSLV06-2
Sample_ID	BGRSLV06-1	BGRSLV06-2
Sample Name	NT-BGRSLV06-1	NT-BGRSLV06-2
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	50,044,141	27,615,191
total_aligned_reads	38,361,497	23,459,205
unique_aligned_reads	36,101,584	22,102,487
percent_uniqueAligned	0.72139	0.80037
correlation_replicates	0.943311	0.943311
spikein_reads	43,688	33,516
percent_spikeins	0.00087	0.00121
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2525	2526

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-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2525	NovaSeq6000	100	paired-ended	1				ENCORE2	8584
NT-BGRSLV06-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2525					GRCh38	V40	NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10449
NT-BGRSLV06-1_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	2525					GRCh38	V40	NT-BGRSLV06-1/Aligned.sortedByCoord.out.bam	ENCORE2	10501
NT-BGRSLV06-1_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	2525					GRCh38	V40	NT-BGRSLV06-1/Aligned.sortedByCoord.out.bam	ENCORE2	10553
NT-BGRSLV06-1_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	2525					GRCh38	V40	NT-BGRSLV06-1/Aligned.sortedByCoord.out.bam	ENCORE2	10605
NT-BGRSLV06-1_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	2525					GRCh38	V40	NT-BGRSLV06-1/Aligned.sortedByCoord.out.bam	ENCORE2	10657
NT-BGRSLV06-1_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2525					GRCh38	V40	NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10709
NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2525	NovaSeq6000	100	paired-ended	2				ENCORE2	28851
NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2526	NovaSeq6000	100	paired-ended	1				ENCORE2	8585
NT-BGRSLV06-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2526					GRCh38	V40	NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10450
NT-BGRSLV06-2_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	2526					GRCh38	V40	NT-BGRSLV06-2/Aligned.sortedByCoord.out.bam	ENCORE2	10502
NT-BGRSLV06-2_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	2526					GRCh38	V40	NT-BGRSLV06-2/Aligned.sortedByCoord.out.bam	ENCORE2	10554
NT-BGRSLV06-2_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	2526					GRCh38	V40	NT-BGRSLV06-2/Aligned.sortedByCoord.out.bam	ENCORE2	10606
NT-BGRSLV06-2_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	2526					GRCh38	V40	NT-BGRSLV06-2/Aligned.sortedByCoord.out.bam	ENCORE2	10658
NT-BGRSLV06-2_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2526					GRCh38	V40	NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10710
NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2526	NovaSeq6000	100	paired-ended	2				ENCORE2	28852