none RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-71	BGRSLV04-72
idx	0	0
TRCN#_or_BGC#
shRNA_or_gRNA_sequence
PAM
Name	baseline	baseline
Sample_ID	BGRSLV04-71	BGRSLV04-72
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	none	none
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
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	8451	8452

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-71	BGRSLV04-72
Sample_ID	BGRSLV04-71	BGRSLV04-72
Sample Name
Sample Name	BL-BGRSLV04-71	BL-BGRSLV04-72
RBP	none	none
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	11474	11475

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-71	BGRSLV04-72
Sample #	3	4
Sample Name	BL-BGRSLV04-71	BL-BGRSLV04-72
Sample_Name_Alias
Index Well Position	C01	D01
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	279	283
Peak_Molarity	26.10	52.40
libSampleQC_DNA_Well	DNA_Library_set59/set1/C7.png	DNA_Library_set59/set1/D7.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set59/set1/C2.png	RNA_Library_set59/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-71	BGRSLV04-72
RBP	BL	BL
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	3552	3553

Sequencing Information

	BGRSLV04-71	BGRSLV04-72
Sample_ID	BGRSLV04-71	BGRSLV04-72
Sample Name	BL-BGRSLV04-71	BL-BGRSLV04-72
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	40,925,928	46,705,308
total_aligned_reads	31,617,791	36,149,211
unique_aligned_reads	29,214,814	33,329,133
percent_uniqueAligned	0.71385	0.71360
correlation_replicates	0.997670	0.997670
spikein_reads	222,492	199,828
percent_spikeins	0.00544	0.00428
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2423	2424

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	Project	FILE_ID
BL-BGRSLV04-71_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2423	NovaSeq6000	100	paired-ended	1				ENCORE2	8050
BL-BGRSLV04-71_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2423	NovaSeq6000	100	paired-ended	2				ENCORE2	8088
BL-BGRSLV04-71_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2423					GRCh38	V40	BL-BGRSLV04-71_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,BL-BGRSLV04-71_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	11019
BL-BGRSLV04-71_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	2423					GRCh38	V40	BL-BGRSLV04-71/Aligned.sortedByCoord.out.bam	ENCORE2	11057
BL-BGRSLV04-71_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	2423					GRCh38	V40	BL-BGRSLV04-71/Aligned.sortedByCoord.out.bam	ENCORE2	11095
BL-BGRSLV04-71_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	2423					GRCh38	V40	BL-BGRSLV04-71/Aligned.sortedByCoord.out.bam	ENCORE2	11133
BL-BGRSLV04-71_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	2423					GRCh38	V40	BL-BGRSLV04-71/Aligned.sortedByCoord.out.bam	ENCORE2	11171
BL-BGRSLV04-71_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2423					GRCh38	V40	BL-BGRSLV04-71_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,BL-BGRSLV04-71_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	11209
BL-BGRSLV04-72_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2424	NovaSeq6000	100	paired-ended	1				ENCORE2	8051
BL-BGRSLV04-72_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2424	NovaSeq6000	100	paired-ended	2				ENCORE2	8089
BL-BGRSLV04-72_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2424					GRCh38	V40	BL-BGRSLV04-72_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,BL-BGRSLV04-72_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	11020
BL-BGRSLV04-72_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	2424					GRCh38	V40	BL-BGRSLV04-72/Aligned.sortedByCoord.out.bam	ENCORE2	11058
BL-BGRSLV04-72_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	2424					GRCh38	V40	BL-BGRSLV04-72/Aligned.sortedByCoord.out.bam	ENCORE2	11096
BL-BGRSLV04-72_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	2424					GRCh38	V40	BL-BGRSLV04-72/Aligned.sortedByCoord.out.bam	ENCORE2	11134
BL-BGRSLV04-72_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	2424					GRCh38	V40	BL-BGRSLV04-72/Aligned.sortedByCoord.out.bam	ENCORE2	11172
BL-BGRSLV04-72_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2424					GRCh38	V40	BL-BGRSLV04-72_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,BL-BGRSLV04-72_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	11210