LIN28B RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-43dox	BGRSDLV02-44dox
idx	0	0
TRCN#_or_BGC#	TRCN0000122599	TRCN0000122599
shRNA_or_gRNA_sequence	CCGGGCCTTGAGTCAATACGGGTAACTCGAGTTACCCGTATTGACTCAAGGCTTTTTTG	CCGGGCCTTGAGTCAATACGGGTAACTCGAGTTACCCGTATTGACTCAAGGCTTTTTTG
PAM
Name	LIN28B	LIN28B
Sample_ID	BGRSDLV02-43dox	BGRSDLV02-44dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	LIN28B	LIN28B
qPCR_result	86.1	83.6
Ave_qPCR	84.9
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	9254	9255

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-43dox	BGRSDLV02-44dox
Sample_ID	BGRSDLV02-43dox	BGRSDLV02-44dox
Sample Name
Sample Name	LIN28B-BGRSDLV02-43dox	LIN28B-BGRSDLV02-44dox
RBP	LIN28B	LIN28B
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12358	12359

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-43dox	BGRSDLV02-44dox
Sample #	39	40
Sample Name	LIN28B-BGRSDLV02-43dox	LIN28B-BGRSDLV02-44dox
Sample_Name_Alias
Index Well Position	G05	H05
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	299	299
Peak_Molarity	76.40	67.70
libSampleQC_DNA_Well	DNA_Library_set65/set1/G5.png	DNA_Library_set65/set1/H5.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set65/set1/G5.png	RNA_Library_set65/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-43dox	BGRSDLV02-44dox
RBP	LIN28B	LIN28B
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	3960	3961

Sequencing Information

	BGRSDLV02-43dox	BGRSDLV02-44dox
Sample_ID	BGRSDLV02-43dox	BGRSDLV02-44dox
Sample Name	LIN28B-BGRSDLV02-43dox	LIN28B-BGRSDLV02-44dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	27,291,940	25,565,557
total_aligned_reads	25,350,774	23,744,704
unique_aligned_reads	23,595,164	22,170,406
percent_uniqueAligned	0.86455	0.86720
correlation_replicates	0.995165	0.995165
spikein_reads	1,094	6,446
percent_spikeins	0.00004	0.00025
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2707	2708

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
LIN28B-BGRSDLV02-43dox_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2707	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8776
LIN28B-BGRSDLV02-43dox_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2707	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8852
LIN28B-BGRSDLV02-43dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2707					GRCh38	V40	LIN28B-BGRSDLV02-43dox_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,LIN28B-BGRSDLV02-43dox_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9341
LIN28B-BGRSDLV02-43dox_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	2707					GRCh38	V40	LIN28B-BGRSDLV02-43dox/Aligned.sortedByCoord.out.bam		ENCORE2	9417
LIN28B-BGRSDLV02-43dox_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	2707					GRCh38	V40	LIN28B-BGRSDLV02-43dox/Aligned.sortedByCoord.out.bam		ENCORE2	9493
LIN28B-BGRSDLV02-43dox_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	2707					GRCh38	V40	LIN28B-BGRSDLV02-43dox/Aligned.sortedByCoord.out.bam		ENCORE2	9569
LIN28B-BGRSDLV02-43dox_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	2707					GRCh38	V40	LIN28B-BGRSDLV02-43dox/Aligned.sortedByCoord.out.bam		ENCORE2	9645
LIN28B-BGRSDLV02-43dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2707					GRCh38	V40	LIN28B-BGRSDLV02-43dox_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,LIN28B-BGRSDLV02-43dox_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9721
LIN28B-BGRSDLV02-44dox_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2708	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8777
LIN28B-BGRSDLV02-44dox_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2708	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8853
LIN28B-BGRSDLV02-44dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2708					GRCh38	V40	LIN28B-BGRSDLV02-44dox_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,LIN28B-BGRSDLV02-44dox_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9342
LIN28B-BGRSDLV02-44dox_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	2708					GRCh38	V40	LIN28B-BGRSDLV02-44dox/Aligned.sortedByCoord.out.bam		ENCORE2	9418
LIN28B-BGRSDLV02-44dox_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	2708					GRCh38	V40	LIN28B-BGRSDLV02-44dox/Aligned.sortedByCoord.out.bam		ENCORE2	9494
LIN28B-BGRSDLV02-44dox_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	2708					GRCh38	V40	LIN28B-BGRSDLV02-44dox/Aligned.sortedByCoord.out.bam		ENCORE2	9570
LIN28B-BGRSDLV02-44dox_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	2708					GRCh38	V40	LIN28B-BGRSDLV02-44dox/Aligned.sortedByCoord.out.bam		ENCORE2	9646
LIN28B-BGRSDLV02-44dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2708					GRCh38	V40	LIN28B-BGRSDLV02-44dox_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,LIN28B-BGRSDLV02-44dox_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9722