GIN1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-29	BGRSLV03-30
idx	0	0
TRCN#_or_BGC#	TRCN0000136811	TRCN0000136811
shRNA_or_gRNA_sequence	CCGGCCTCTGGAACTGTTAACCCAACTCGAGTTGGGTTAACAGTTCCAGAGGTTTTTTG	CCGGCCTCTGGAACTGTTAACCCAACTCGAGTTGGGTTAACAGTTCCAGAGGTTTTTTG
PAM
Name	GIN1	GIN1
Sample_ID	BGRSLV03-29	BGRSLV03-30
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	GIN1	GIN1
qPCR_result	62.4	64.9
Ave_qPCR	63.6
RT-qPCR_primer-F	ccaggaccctcactctggta
RT-qPCR_primer-R	aggtgctgtttcggtgctac
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	8339	8340

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-29	BGRSLV03-30
Sample_ID	BGRSLV03-29	BGRSLV03-30
Sample Name
Sample Name	GIN1-BGRSLV03-29	GIN1-BGRSLV03-30
RBP	GIN1	GIN1
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	11390	11391

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-29	BGRSLV03-30
Sample #	21	22
Sample Name	GIN1-BGRSLV03-29	GIN1-BGRSLV03-30
Sample_Name_Alias
Index Well Position	E09	F09
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	294	296
Peak_Molarity	75.50	79.80
libSampleQC_DNA_Well	DNA_Library_set58/set1/E9.png	DNA_Library_set58/set1/F9.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set58/set1/E3.png	RNA_Library_set58/set1/F3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-29	BGRSLV03-30
RBP	GIN1	GIN1
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	3528	3529

Sequencing Information

	BGRSLV03-29	BGRSLV03-30
Sample_ID	BGRSLV03-29	BGRSLV03-30
Sample Name	GIN1-BGRSLV03-29	GIN1-BGRSLV03-30
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	56,472,423	42,996,601
total_aligned_reads	49,948,132	35,539,264
unique_aligned_reads	46,516,585	33,104,096
percent_uniqueAligned	0.82370	0.76992
correlation_replicates	0.990574	0.990574
spikein_reads	353,444	229,476
percent_spikeins	0.00626	0.00534
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2399	2400

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
GIN1-BGRSLV03-29_S155_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2399	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	8144
GIN1-BGRSLV03-29_S155_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2399	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	8186
GIN1-BGRSLV03-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2399					GRCh38	V40	GIN1-BGRSLV03-29_S155_L004_R1_001.filtered.trimmed.paired.fastq.gz,GIN1-BGRSLV03-29_S155_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11265
GIN1-BGRSLV03-29_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	2399					GRCh38	V40	GIN1-BGRSLV03-29/Aligned.sortedByCoord.out.bam		ENCORE2	11307
GIN1-BGRSLV03-29_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	2399					GRCh38	V40	GIN1-BGRSLV03-29/Aligned.sortedByCoord.out.bam		ENCORE2	11349
GIN1-BGRSLV03-29_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	2399					GRCh38	V40	GIN1-BGRSLV03-29/Aligned.sortedByCoord.out.bam		ENCORE2	11391
GIN1-BGRSLV03-29_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	2399					GRCh38	V40	GIN1-BGRSLV03-29/Aligned.sortedByCoord.out.bam		ENCORE2	11433
GIN1-BGRSLV03-29_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2399					GRCh38	V40	GIN1-BGRSLV03-29_S155_L004_R1_001.filtered.trimmed.paired.fastq.gz,GIN1-BGRSLV03-29_S155_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11475
GIN1-BGRSLV03-30_S156_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2400	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	8145
GIN1-BGRSLV03-30_S156_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2400	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	8187
GIN1-BGRSLV03-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2400					GRCh38	V40	GIN1-BGRSLV03-30_S156_L004_R1_001.filtered.trimmed.paired.fastq.gz,GIN1-BGRSLV03-30_S156_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11266
GIN1-BGRSLV03-30_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	2400					GRCh38	V40	GIN1-BGRSLV03-30/Aligned.sortedByCoord.out.bam		ENCORE2	11308
GIN1-BGRSLV03-30_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	2400					GRCh38	V40	GIN1-BGRSLV03-30/Aligned.sortedByCoord.out.bam		ENCORE2	11350
GIN1-BGRSLV03-30_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	2400					GRCh38	V40	GIN1-BGRSLV03-30/Aligned.sortedByCoord.out.bam		ENCORE2	11392
GIN1-BGRSLV03-30_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	2400					GRCh38	V40	GIN1-BGRSLV03-30/Aligned.sortedByCoord.out.bam		ENCORE2	11434
GIN1-BGRSLV03-30_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2400					GRCh38	V40	GIN1-BGRSLV03-30_S156_L004_R1_001.filtered.trimmed.paired.fastq.gz,GIN1-BGRSLV03-30_S156_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11476