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

General Information

List KD experiments controlled by BGRSLV05-1 and BGRSLV05-2

NT-BGRSLV05-1,NT-BGRSLV05-2:

RNF150-BGRSLV05-RS293

TRIM32-BGRSLV05-RS293

TRMU-BGRSLV05-RS293

U2AF1L4-BGRSLV05-RS293

USP39-BGRSLV05-RS293

ZCCHC9-BGRSLV05-RS293

ZCRB1-BGRSLV05-RS293

ZCWPW1-BGRSLV05-RS293

ZDHHC5-BGRSLV05-RS293

ZMAT2-BGRSLV05-RS293

Experiment Information (Status: Submitted)

	BGRSLV05-1	BGRSLV05-2
idx	0	0
TRCN#_or_BGC#	SHC002	SHC002
shRNA_or_gRNA_sequence	CAACAAGATGAAGAGCACCAA	CAACAAGATGAAGAGCACCAA
PAM
Name	non-target	non-target
Sample_ID	BGRSLV05-1	BGRSLV05-2
transduction_Date	3/2/23	3/2/23
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	8454	8455

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV05-1	BGRSLV05-2
Sample_ID	BGRSLV05-1	BGRSLV05-2
Sample Name
Sample Name	NT-BGRSLV05-1	NT-BGRSLV05-2
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	11612	11613

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV05-1	BGRSLV05-2
Sample #	45	46
Sample Name	NT-BGRSLV05-1	NT-BGRSLV05-2
Sample_Name_Alias
Index Well Position	E06	F06
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	294	307
Peak_Molarity	35.80	70.30
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/A7.png	DNA_Library_set60-62/set1/B7.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set60-62/set1/E6.png	RNA_Library_set60-62/set1/F6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV05-1	BGRSLV05-2
RBP	NT	NT
Batch_ID	BGRSLV05	BGRSLV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3632	3633

Sequencing Information

	BGRSLV05-1	BGRSLV05-2
Sample_ID	BGRSLV05-1	BGRSLV05-2
Sample Name	NT-BGRSLV05-1	NT-BGRSLV05-2
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	55,010,464	37,384,276
total_aligned_reads	45,264,536	32,781,037
unique_aligned_reads	41,885,637	30,533,155
percent_uniqueAligned	0.76141	0.81674
correlation_replicates	0.985240	0.985240
spikein_reads	218,462	132,298
percent_spikeins	0.00397	0.00354
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2503	2504

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-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2503	NovaSeq6000	100	paired-ended	1				ENCORE2	8582
NT-BGRSLV05-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2503					GRCh38	V40	NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10447
NT-BGRSLV05-1_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	2503					GRCh38	V40	NT-BGRSLV05-1/Aligned.sortedByCoord.out.bam	ENCORE2	10499
NT-BGRSLV05-1_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	2503					GRCh38	V40	NT-BGRSLV05-1/Aligned.sortedByCoord.out.bam	ENCORE2	10551
NT-BGRSLV05-1_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	2503					GRCh38	V40	NT-BGRSLV05-1/Aligned.sortedByCoord.out.bam	ENCORE2	10603
NT-BGRSLV05-1_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	2503					GRCh38	V40	NT-BGRSLV05-1/Aligned.sortedByCoord.out.bam	ENCORE2	10655
NT-BGRSLV05-1_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2503					GRCh38	V40	NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10707
NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2503	NovaSeq6000	100	paired-ended	2				ENCORE2	28849
NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2504	NovaSeq6000	100	paired-ended	1				ENCORE2	8583
NT-BGRSLV05-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2504					GRCh38	V40	NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10448
NT-BGRSLV05-2_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	2504					GRCh38	V40	NT-BGRSLV05-2/Aligned.sortedByCoord.out.bam	ENCORE2	10500
NT-BGRSLV05-2_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	2504					GRCh38	V40	NT-BGRSLV05-2/Aligned.sortedByCoord.out.bam	ENCORE2	10552
NT-BGRSLV05-2_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	2504					GRCh38	V40	NT-BGRSLV05-2/Aligned.sortedByCoord.out.bam	ENCORE2	10604
NT-BGRSLV05-2_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	2504					GRCh38	V40	NT-BGRSLV05-2/Aligned.sortedByCoord.out.bam	ENCORE2	10656
NT-BGRSLV05-2_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2504					GRCh38	V40	NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10708
NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2504	NovaSeq6000	100	paired-ended	2				ENCORE2	28850