NR5A2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-39	BGRSLV03-40
idx	0	0
TRCN#_or_BGC#	TRCN0000019654	TRCN0000019654
shRNA_or_gRNA_sequence	CCGGCCGAGTCCATAATGGGCTATTCTCGAGAATAGCCCATTATGGACTCGGTTTTT	CCGGCCGAGTCCATAATGGGCTATTCTCGAGAATAGCCCATTATGGACTCGGTTTTT
PAM
Name	NR5A2	NR5A2
Sample_ID	BGRSLV03-39	BGRSLV03-40
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	NR5A2	NR5A2
qPCR_result	65.8	64.0
Ave_qPCR	64.9
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	8349	8350

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-39	BGRSLV03-40
Sample_ID	BGRSLV03-39	BGRSLV03-40
Sample Name
Sample Name	NR5A2-BGRSLV03-39	NR5A2-BGRSLV03-40
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	11392	11393

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-39	BGRSLV03-40
Sample #	23	24
Sample Name	NR5A2-BGRSLV03-39	NR5A2-BGRSLV03-40
Sample_Name_Alias
Index Well Position	G09	H09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	298	300
Peak_Molarity	72.00	49.40
libSampleQC_DNA_Well	DNA_Library_set58/set1/G9.png	DNA_Library_set58/set1/H9.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set58/set1/G3.png	RNA_Library_set58/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-39	BGRSLV03-40
RBP	NR5A2	NR5A2
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3530	3531

Sequencing Information

	BGRSLV03-39	BGRSLV03-40
Sample_ID	BGRSLV03-39	BGRSLV03-40
Sample Name	NR5A2-BGRSLV03-39	NR5A2-BGRSLV03-40
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	51,237,635	64,770,652
total_aligned_reads	38,100,454	57,365,946
unique_aligned_reads	35,411,884	53,205,382
percent_uniqueAligned	0.69113	0.82144
correlation_replicates	0.960977	0.960977
spikein_reads	244,928	376,002
percent_spikeins	0.00478	0.00581
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2401	2402

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-BGRSLV03-39_S157_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2401	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8146
NR5A2-BGRSLV03-39_S157_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2401	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8188
NR5A2-BGRSLV03-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2401					GRCh38	V40	NR5A2-BGRSLV03-39_S157_L004_R1_001.filtered.trimmed.paired.fastq.gz,NR5A2-BGRSLV03-39_S157_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11267
NR5A2-BGRSLV03-39_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2401					GRCh38	V40	NR5A2-BGRSLV03-39/Aligned.sortedByCoord.out.bam		ENCORE2	11309
NR5A2-BGRSLV03-39_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2401					GRCh38	V40	NR5A2-BGRSLV03-39/Aligned.sortedByCoord.out.bam		ENCORE2	11351
NR5A2-BGRSLV03-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2401					GRCh38	V40	NR5A2-BGRSLV03-39/Aligned.sortedByCoord.out.bam		ENCORE2	11393
NR5A2-BGRSLV03-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2401					GRCh38	V40	NR5A2-BGRSLV03-39/Aligned.sortedByCoord.out.bam		ENCORE2	11435
NR5A2-BGRSLV03-39_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2401					GRCh38	V40	NR5A2-BGRSLV03-39_S157_L004_R1_001.filtered.trimmed.paired.fastq.gz,NR5A2-BGRSLV03-39_S157_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11477
NR5A2-BGRSLV03-40_S158_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2402	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8147
NR5A2-BGRSLV03-40_S158_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2402	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8189
NR5A2-BGRSLV03-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2402					GRCh38	V40	NR5A2-BGRSLV03-40_S158_L004_R1_001.filtered.trimmed.paired.fastq.gz,NR5A2-BGRSLV03-40_S158_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11268
NR5A2-BGRSLV03-40_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2402					GRCh38	V40	NR5A2-BGRSLV03-40/Aligned.sortedByCoord.out.bam		ENCORE2	11310
NR5A2-BGRSLV03-40_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2402					GRCh38	V40	NR5A2-BGRSLV03-40/Aligned.sortedByCoord.out.bam		ENCORE2	11352
NR5A2-BGRSLV03-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2402					GRCh38	V40	NR5A2-BGRSLV03-40/Aligned.sortedByCoord.out.bam		ENCORE2	11394
NR5A2-BGRSLV03-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2402					GRCh38	V40	NR5A2-BGRSLV03-40/Aligned.sortedByCoord.out.bam		ENCORE2	11436
NR5A2-BGRSLV03-40_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2402					GRCh38	V40	NR5A2-BGRSLV03-40_S158_L004_R1_001.filtered.trimmed.paired.fastq.gz,NR5A2-BGRSLV03-40_S158_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11478