NR5A2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-25	BGRSLV02-26
idx	0	0
TRCN#_or_BGC#	TRCN0000019656	TRCN0000019656
shRNA_or_gRNA_sequence	CCGGGCGTTGTCCTTACTGTCGTTTCTCGAGAAACGACAGTAAGGACAACGCTTTTT	CCGGGCGTTGTCCTTACTGTCGTTTCTCGAGAAACGACAGTAAGGACAACGCTTTTT
PAM
Name	NR5A2	NR5A2
Sample_ID	BGRSLV02-25	BGRSLV02-26
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	NR5A2	NR5A2
qPCR_result	86.0	84.8
Ave_qPCR	85.4
RT-qPCR_primer-F	atcctcgaccacatttaccg
RT-qPCR_primer-R	tgccactaactcctgtgcat
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	8262	8263

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-25	BGRSLV02-26
Sample_ID	BGRSLV02-25	BGRSLV02-26
Sample Name
Sample Name	NR5A2-BGRSLV02-25	NR5A2-BGRSLV02-26
RBP	NR5A2	NR5A2
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	11312	11313

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-25	BGRSLV02-26
Sample #	15	16
Sample Name	NR5A2-BGRSLV02-25	NR5A2-BGRSLV02-26
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	287	284
Peak_Molarity	34.20	63.20
libSampleQC_DNA_Well	DNA_Library_set57/set1/G8.png	DNA_Library_set57/set1/H8.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set57/set1/G2.png	RNA_Library_set57/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-25	BGRSLV02-26
RBP	NR5A2	NR5A2
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3476	3477

Sequencing Information

	BGRSLV02-25	BGRSLV02-26
Sample_ID	BGRSLV02-25	BGRSLV02-26
Sample Name	NR5A2-BGRSLV02-25	NR5A2-BGRSLV02-26
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	61,641,281	39,304,497
total_aligned_reads	54,503,595	36,159,697
unique_aligned_reads	50,981,596	33,875,890
percent_uniqueAligned	0.82707	0.86188
correlation_replicates	0.970945	0.970945
spikein_reads	22,966	22,962
percent_spikeins	0.00037	0.00058
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2347	2348

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
NR5A2-BGRSLV02-25_S103_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2347	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8222
NR5A2-BGRSLV02-25_S103_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2347	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8268
NR5A2-BGRSLV02-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2347					GRCh38	V40	NR5A2-BGRSLV02-25_S103_L003_R1_001.filtered.trimmed.paired.fastq.gz,NR5A2-BGRSLV02-25_S103_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11511
NR5A2-BGRSLV02-25_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2347					GRCh38	V40	NR5A2-BGRSLV02-25/Aligned.sortedByCoord.out.bam		ENCORE2	11557
NR5A2-BGRSLV02-25_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2347					GRCh38	V40	NR5A2-BGRSLV02-25/Aligned.sortedByCoord.out.bam		ENCORE2	11603
NR5A2-BGRSLV02-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2347					GRCh38	V40	NR5A2-BGRSLV02-25/Aligned.sortedByCoord.out.bam		ENCORE2	11649
NR5A2-BGRSLV02-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2347					GRCh38	V40	NR5A2-BGRSLV02-25/Aligned.sortedByCoord.out.bam		ENCORE2	11695
NR5A2-BGRSLV02-25_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2347					GRCh38	V40	NR5A2-BGRSLV02-25_S103_L003_R1_001.filtered.trimmed.paired.fastq.gz,NR5A2-BGRSLV02-25_S103_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11741
NR5A2-BGRSLV02-26_S104_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2348	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8223
NR5A2-BGRSLV02-26_S104_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2348	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8269
NR5A2-BGRSLV02-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2348					GRCh38	V40	NR5A2-BGRSLV02-26_S104_L003_R1_001.filtered.trimmed.paired.fastq.gz,NR5A2-BGRSLV02-26_S104_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11512
NR5A2-BGRSLV02-26_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2348					GRCh38	V40	NR5A2-BGRSLV02-26/Aligned.sortedByCoord.out.bam		ENCORE2	11558
NR5A2-BGRSLV02-26_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2348					GRCh38	V40	NR5A2-BGRSLV02-26/Aligned.sortedByCoord.out.bam		ENCORE2	11604
NR5A2-BGRSLV02-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2348					GRCh38	V40	NR5A2-BGRSLV02-26/Aligned.sortedByCoord.out.bam		ENCORE2	11650
NR5A2-BGRSLV02-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2348					GRCh38	V40	NR5A2-BGRSLV02-26/Aligned.sortedByCoord.out.bam		ENCORE2	11696
NR5A2-BGRSLV02-26_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2348					GRCh38	V40	NR5A2-BGRSLV02-26_S104_L003_R1_001.filtered.trimmed.paired.fastq.gz,NR5A2-BGRSLV02-26_S104_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11742