BRCA1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-9	BGRSDLV02-10
idx	0	0
TRCN#_or_BGC#	TRCN0000244986	TRCN0000244986
shRNA_or_gRNA_sequence	CCGGTTGCAACCTGAGGTCTATAAACTCGAGTTTATAGACCTCAGGTTGCAATTTTTG	CCGGTTGCAACCTGAGGTCTATAAACTCGAGTTTATAGACCTCAGGTTGCAATTTTTG
PAM
Name	BRCA1	BRCA1
Sample_ID	BGRSDLV02-9	BGRSDLV02-10
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	BRCA1	BRCA1
qPCR_result	64.5	67.4
Ave_qPCR	66.0
RT-qPCR_primer-F	ttgatgtggaggagcaacag
RT-qPCR_primer-R	gaggctgattccagattcca
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	9220	9221

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-9	BGRSDLV02-10
Sample_ID	BGRSDLV02-9	BGRSDLV02-10
Sample Name
Sample Name	BRCA1-BGRSDLV02-9	BRCA1-BGRSDLV02-10
RBP	BRCA1	BRCA1
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12328	12329

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-9	BGRSDLV02-10
Sample #	9	10
Sample Name	BRCA1-BGRSDLV02-9	BRCA1-BGRSDLV02-10
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-26	2023-09-26
Lib_ID	Lib-230926	Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp	289	286
Peak_Molarity	79.70	71.70
libSampleQC_DNA_Well	DNA_Library_set65/set1/A2.png	DNA_Library_set65/set1/B2.png
RIN	9.8	9.5
libSample_RNA_Well	RNA_Library_set65/set1/A2.png	RNA_Library_set65/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-9	BGRSDLV02-10
RBP	BRCA1	BRCA1
Batch_ID	BGRSDLV02	BGRSDLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3930	3931

Sequencing Information

	BGRSDLV02-9	BGRSDLV02-10
Sample_ID	BGRSDLV02-9	BGRSDLV02-10
Sample Name	BRCA1-BGRSDLV02-9	BRCA1-BGRSDLV02-10
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	29,380,616	27,070,431
total_aligned_reads	25,283,127	23,399,524
unique_aligned_reads	23,467,414	21,668,008
percent_uniqueAligned	0.79874	0.80043
correlation_replicates	0.978997	0.978997
spikein_reads	13,792	6,164
percent_spikeins	0.00047	0.00023
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2677	2678

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
BRCA1-BGRSDLV02-9_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2677	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8745
BRCA1-BGRSDLV02-9_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2677	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8821
BRCA1-BGRSDLV02-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2677					GRCh38	V40	BRCA1-BGRSDLV02-9_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRCA1-BGRSDLV02-9_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9310
BRCA1-BGRSDLV02-9_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2677					GRCh38	V40	BRCA1-BGRSDLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	9386
BRCA1-BGRSDLV02-9_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2677					GRCh38	V40	BRCA1-BGRSDLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	9462
BRCA1-BGRSDLV02-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2677					GRCh38	V40	BRCA1-BGRSDLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	9538
BRCA1-BGRSDLV02-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2677					GRCh38	V40	BRCA1-BGRSDLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	9614
BRCA1-BGRSDLV02-9_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2677					GRCh38	V40	BRCA1-BGRSDLV02-9_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRCA1-BGRSDLV02-9_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9690
BRCA1-BGRSDLV02-10_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2678	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8742
BRCA1-BGRSDLV02-10_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2678	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8818
BRCA1-BGRSDLV02-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2678					GRCh38	V40	BRCA1-BGRSDLV02-10_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRCA1-BGRSDLV02-10_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9307
BRCA1-BGRSDLV02-10_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2678					GRCh38	V40	BRCA1-BGRSDLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	9383
BRCA1-BGRSDLV02-10_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2678					GRCh38	V40	BRCA1-BGRSDLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	9459
BRCA1-BGRSDLV02-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2678					GRCh38	V40	BRCA1-BGRSDLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	9535
BRCA1-BGRSDLV02-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2678					GRCh38	V40	BRCA1-BGRSDLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	9611
BRCA1-BGRSDLV02-10_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2678					GRCh38	V40	BRCA1-BGRSDLV02-10_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRCA1-BGRSDLV02-10_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9687