NR3C1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV06-11	BGRSLV06-12
idx	0	0
TRCN#_or_BGC#	TRCN0000245004	TRCN0000245004
shRNA_or_gRNA_sequence	CCGGGTGTCACTGTTGGAGGTTATTCTCGAGAATAACCTCCAACAGTGACACTTTTTG	CCGGGTGTCACTGTTGGAGGTTATTCTCGAGAATAACCTCCAACAGTGACACTTTTTG
PAM
Name	NR3C1	NR3C1
Sample_ID	BGRSLV06-11	BGRSLV06-12
transduction_Date	3/27/23	3/27/23
days	D4	D4
RBP_name	NR3C1	NR3C1
qPCR_result	64.2	69.2
Ave_qPCR	66.7
RT-qPCR_primer-F	taccctgcatgtacgaccaa
RT-qPCR_primer-R	ggctcttcagaccgtcctta
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	8538	8539

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV06-11	BGRSLV06-12
Sample_ID	BGRSLV06-11	BGRSLV06-12
Sample Name
Sample Name	NR3C1-BGRSLV06-11	NR3C1-BGRSLV06-12
RBP	NR3C1	NR3C1
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	11688	11689

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV06-11	BGRSLV06-12
Sample #	71	72
Sample Name	NR3C1-BGRSLV06-11	NR3C1-BGRSLV06-12
Sample_Name_Alias
Index Well Position	G09	H09
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	285	286
Peak_Molarity	128.00	95.50
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/C10.png	DNA_Library_set60-62/set1/D10.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set60-62/set1/G9.png	RNA_Library_set60-62/set1/H9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV06-11	BGRSLV06-12
RBP	NR3C1	NR3C1
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	3658	3659

Sequencing Information

	BGRSLV06-11	BGRSLV06-12
Sample_ID	BGRSLV06-11	BGRSLV06-12
Sample Name	NR3C1-BGRSLV06-11	NR3C1-BGRSLV06-12
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	31,569,876	38,670,992
total_aligned_reads	27,517,804	28,083,408
unique_aligned_reads	25,913,329	26,430,711
percent_uniqueAligned	0.82082	0.68348
correlation_replicates	0.993892	0.993892
spikein_reads	54,262	39,356
percent_spikeins	0.00172	0.00102
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2529	2530

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
NR3C1-BGRSLV06-11_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2529	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8580
NR3C1-BGRSLV06-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2529					GRCh38	V40	NR3C1-BGRSLV06-11_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz,NR3C1-BGRSLV06-11_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10445
NR3C1-BGRSLV06-11_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	2529					GRCh38	V40	NR3C1-BGRSLV06-11/Aligned.sortedByCoord.out.bam		ENCORE2	10497
NR3C1-BGRSLV06-11_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	2529					GRCh38	V40	NR3C1-BGRSLV06-11/Aligned.sortedByCoord.out.bam		ENCORE2	10549
NR3C1-BGRSLV06-11_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	2529					GRCh38	V40	NR3C1-BGRSLV06-11/Aligned.sortedByCoord.out.bam		ENCORE2	10601
NR3C1-BGRSLV06-11_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	2529					GRCh38	V40	NR3C1-BGRSLV06-11/Aligned.sortedByCoord.out.bam		ENCORE2	10653
NR3C1-BGRSLV06-11_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2529					GRCh38	V40	NR3C1-BGRSLV06-11_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz,NR3C1-BGRSLV06-11_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10705
NR3C1-BGRSLV06-11_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2529	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28847
NR3C1-BGRSLV06-12_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2530	NovaSeq6000	100	paired-ended	1				NT-BGRSLV06-1_S67_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8581
NR3C1-BGRSLV06-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2530					GRCh38	V40	NR3C1-BGRSLV06-12_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz,NR3C1-BGRSLV06-12_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10446
NR3C1-BGRSLV06-12_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	2530					GRCh38	V40	NR3C1-BGRSLV06-12/Aligned.sortedByCoord.out.bam		ENCORE2	10498
NR3C1-BGRSLV06-12_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	2530					GRCh38	V40	NR3C1-BGRSLV06-12/Aligned.sortedByCoord.out.bam		ENCORE2	10550
NR3C1-BGRSLV06-12_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	2530					GRCh38	V40	NR3C1-BGRSLV06-12/Aligned.sortedByCoord.out.bam		ENCORE2	10602
NR3C1-BGRSLV06-12_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	2530					GRCh38	V40	NR3C1-BGRSLV06-12/Aligned.sortedByCoord.out.bam		ENCORE2	10654
NR3C1-BGRSLV06-12_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2530					GRCh38	V40	NR3C1-BGRSLV06-12_S72_L002_R1_001.filtered.trimmed.paired.fastq.gz,NR3C1-BGRSLV06-12_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10706
NR3C1-BGRSLV06-12_S72_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2530	NovaSeq6000	100	paired-ended	2				NT-BGRSLV06-1_S67_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV06-2_S68_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28848