ZMAT2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV05-67	BGRSLV05-68
idx	0	0
TRCN#_or_BGC#	TRCN0000001206	TRCN0000001206
shRNA_or_gRNA_sequence	CCGGGAGAAGCAGAAGGATTATGATCTCGAGATCATAATCCTTCTGCTTCTCTTTTT	CCGGGAGAAGCAGAAGGATTATGATCTCGAGATCATAATCCTTCTGCTTCTCTTTTT
PAM
Name	ZMAT2	ZMAT2
Sample_ID	BGRSLV05-67	BGRSLV05-68
transduction_Date	3/2/23	3/2/23
days	D4	D4
RBP_name	ZMAT2	ZMAT2
qPCR_result	92.0	95.2
Ave_qPCR	93.6
RT-qPCR_primer-F	gagaagaggctcacggaaga
RT-qPCR_primer-R	aaaagctctcgcttgacagg
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	8520	8521

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV05-67	BGRSLV05-68
Sample_ID	BGRSLV05-67	BGRSLV05-68
Sample Name
Sample Name	ZMAT2-BGRSLV05-67	ZMAT2-BGRSLV05-68
RBP	ZMAT2	ZMAT2
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	11632	11633

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV05-67	BGRSLV05-68
Sample #	65	66
Sample Name	ZMAT2-BGRSLV05-67	ZMAT2-BGRSLV05-68
Sample_Name_Alias
Index Well Position	A09	B09
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	284	293
Peak_Molarity	98.60	98.10
libSampleQC_DNA_Well	DNA_Library_set60-62/set1/E9.png	DNA_Library_set60-62/set1/F9.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set60-62/set1/A9.png	RNA_Library_set60-62/set1/B9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BGRSLV05-67	BGRSLV05-68
RBP	ZMAT2	ZMAT2
Batch_ID	BGRSLV05	BGRSLV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3652	3653

Sequencing Information

	BGRSLV05-67	BGRSLV05-68
Sample_ID	BGRSLV05-67	BGRSLV05-68
Sample Name	ZMAT2-BGRSLV05-67	ZMAT2-BGRSLV05-68
Pool ID	Pool-230417B	Pool-230417B
LocalServer_folder	set61	set61
total_reads	39,827,097	45,983,486
total_aligned_reads	22,247,318	26,799,943
unique_aligned_reads	20,685,737	24,921,308
percent_uniqueAligned	0.51939	0.54196
correlation_replicates	0.973442	0.973442
spikein_reads	58,034	51,354
percent_spikeins	0.00146	0.00112
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2523	2524

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
ZMAT2-BGRSLV05-67_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2523	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8624
ZMAT2-BGRSLV05-67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2523					GRCh38	V40	ZMAT2-BGRSLV05-67_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT2-BGRSLV05-67_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10489
ZMAT2-BGRSLV05-67_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	2523					GRCh38	V40	ZMAT2-BGRSLV05-67/Aligned.sortedByCoord.out.bam		ENCORE2	10541
ZMAT2-BGRSLV05-67_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	2523					GRCh38	V40	ZMAT2-BGRSLV05-67/Aligned.sortedByCoord.out.bam		ENCORE2	10593
ZMAT2-BGRSLV05-67_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	2523					GRCh38	V40	ZMAT2-BGRSLV05-67/Aligned.sortedByCoord.out.bam		ENCORE2	10645
ZMAT2-BGRSLV05-67_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	2523					GRCh38	V40	ZMAT2-BGRSLV05-67/Aligned.sortedByCoord.out.bam		ENCORE2	10697
ZMAT2-BGRSLV05-67_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2523					GRCh38	V40	ZMAT2-BGRSLV05-67_S65_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT2-BGRSLV05-67_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10749
ZMAT2-BGRSLV05-67_S65_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2523	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28891
ZMAT2-BGRSLV05-68_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2524	NovaSeq6000	100	paired-ended	1				NT-BGRSLV05-1_S45_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8625
ZMAT2-BGRSLV05-68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set61/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2524					GRCh38	V40	ZMAT2-BGRSLV05-68_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT2-BGRSLV05-68_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10490
ZMAT2-BGRSLV05-68_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	2524					GRCh38	V40	ZMAT2-BGRSLV05-68/Aligned.sortedByCoord.out.bam		ENCORE2	10542
ZMAT2-BGRSLV05-68_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	2524					GRCh38	V40	ZMAT2-BGRSLV05-68/Aligned.sortedByCoord.out.bam		ENCORE2	10594
ZMAT2-BGRSLV05-68_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	2524					GRCh38	V40	ZMAT2-BGRSLV05-68/Aligned.sortedByCoord.out.bam		ENCORE2	10646
ZMAT2-BGRSLV05-68_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	2524					GRCh38	V40	ZMAT2-BGRSLV05-68/Aligned.sortedByCoord.out.bam		ENCORE2	10698
ZMAT2-BGRSLV05-68_quant.sf	ENCODE_DATA/set61/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2524					GRCh38	V40	ZMAT2-BGRSLV05-68_S66_L002_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT2-BGRSLV05-68_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10750
ZMAT2-BGRSLV05-68_S66_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set61/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2524	NovaSeq6000	100	paired-ended	2				NT-BGRSLV05-1_S45_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV05-2_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28892