LYAR RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-17	BGRSLV04-18
idx	0	0
TRCN#_or_BGC#	TRCN0000072303	TRCN0000072303
shRNA_or_gRNA_sequence	CCGGTCTTCCTTTCACTGCTGTTTACTCGAGTAAACAGCAGTGAAAGGAAGATTTTTG	CCGGTCTTCCTTTCACTGCTGTTTACTCGAGTAAACAGCAGTGAAAGGAAGATTTTTG
PAM
Name	LYAR	LYAR
Sample_ID	BGRSLV04-17	BGRSLV04-18
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	LYAR	LYAR
qPCR_result	54.7	67.6
Ave_qPCR	61.1
RT-qPCR_primer-F	ttctggaccaggtgtggaat
RT-qPCR_primer-R	actttggaggctggaacctt
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	8397	8398

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-17	BGRSLV04-18
Sample_ID	BGRSLV04-17	BGRSLV04-18
Sample Name
Sample Name	LYAR-BGRSLV04-17	LYAR-BGRSLV04-18
RBP	LYAR	LYAR
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	11444	11445

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-17	BGRSLV04-18
Sample #	9	10
Sample Name	LYAR-BGRSLV04-17	LYAR-BGRSLV04-18
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-03-02	2023-03-02
Lib_ID	Lib-230302	Lib-230302
Tecan_Location
Tecan
Tecan_date
Size_bp	296	291
Peak_Molarity	34.20	47.80
libSampleQC_DNA_Well	DNA_Library_set59/set1/A8.png	DNA_Library_set59/set1/B8.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set59/set1/A3.png	RNA_Library_set59/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-17	BGRSLV04-18
RBP	LYAR	LYAR
Batch_ID	BGRSLV04	BGRSLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3558	3559

Sequencing Information

	BGRSLV04-17	BGRSLV04-18
Sample_ID	BGRSLV04-17	BGRSLV04-18
Sample Name	LYAR-BGRSLV04-17	LYAR-BGRSLV04-18
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	34,506,575	48,046,337
total_aligned_reads	24,144,107	38,382,251
unique_aligned_reads	22,366,871	35,408,278
percent_uniqueAligned	0.64819	0.73696
correlation_replicates	0.991813	0.991813
spikein_reads	167,664	250,794
percent_spikeins	0.00486	0.00522
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2429	2430

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
LYAR-BGRSLV04-17_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2429	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8056
LYAR-BGRSLV04-17_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2429	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8094
LYAR-BGRSLV04-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2429					GRCh38	V40	LYAR-BGRSLV04-17_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,LYAR-BGRSLV04-17_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11025
LYAR-BGRSLV04-17_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2429					GRCh38	V40	LYAR-BGRSLV04-17/Aligned.sortedByCoord.out.bam		ENCORE2	11063
LYAR-BGRSLV04-17_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2429					GRCh38	V40	LYAR-BGRSLV04-17/Aligned.sortedByCoord.out.bam		ENCORE2	11101
LYAR-BGRSLV04-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2429					GRCh38	V40	LYAR-BGRSLV04-17/Aligned.sortedByCoord.out.bam		ENCORE2	11139
LYAR-BGRSLV04-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2429					GRCh38	V40	LYAR-BGRSLV04-17/Aligned.sortedByCoord.out.bam		ENCORE2	11177
LYAR-BGRSLV04-17_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2429					GRCh38	V40	LYAR-BGRSLV04-17_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,LYAR-BGRSLV04-17_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11215
LYAR-BGRSLV04-18_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2430	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8057
LYAR-BGRSLV04-18_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2430	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8095
LYAR-BGRSLV04-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2430					GRCh38	V40	LYAR-BGRSLV04-18_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,LYAR-BGRSLV04-18_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11026
LYAR-BGRSLV04-18_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2430					GRCh38	V40	LYAR-BGRSLV04-18/Aligned.sortedByCoord.out.bam		ENCORE2	11064
LYAR-BGRSLV04-18_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2430					GRCh38	V40	LYAR-BGRSLV04-18/Aligned.sortedByCoord.out.bam		ENCORE2	11102
LYAR-BGRSLV04-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2430					GRCh38	V40	LYAR-BGRSLV04-18/Aligned.sortedByCoord.out.bam		ENCORE2	11140
LYAR-BGRSLV04-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2430					GRCh38	V40	LYAR-BGRSLV04-18/Aligned.sortedByCoord.out.bam		ENCORE2	11178
LYAR-BGRSLV04-18_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2430					GRCh38	V40	LYAR-BGRSLV04-18_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,LYAR-BGRSLV04-18_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11216