ZMAT3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-53	BGRSLV03-54
idx	0	0
TRCN#_or_BGC#	TRCN0000128165	TRCN0000128165
shRNA_or_gRNA_sequence	CCGGCATGGTAAGAAACTCCGAAATCTCGAGATTTCGGAGTTTCTTACCATGTTTTTTG	CCGGCATGGTAAGAAACTCCGAAATCTCGAGATTTCGGAGTTTCTTACCATGTTTTTTG
PAM
Name	ZMAT3	ZMAT3
Sample_ID	BGRSLV03-53	BGRSLV03-54
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	ZMAT3	ZMAT3
qPCR_result	56.2	56.6
Ave_qPCR	56.4
RT-qPCR_primer-F	gggaagaatcatgccaagag
RT-qPCR_primer-R	ttgacccagctctgaggatt
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	8363	8364

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-53	BGRSLV03-54
Sample_ID	BGRSLV03-53	BGRSLV03-54
Sample Name
Sample Name	ZMAT3-BGRSLV03-53	ZMAT3-BGRSLV03-54
RBP	ZMAT3	ZMAT3
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	11400	11401

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-53	BGRSLV03-54
Sample #	31	32
Sample Name	ZMAT3-BGRSLV03-53	ZMAT3-BGRSLV03-54
Sample_Name_Alias
Index Well Position	G10	H10
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	295	306
Peak_Molarity	103.00	67.10
libSampleQC_DNA_Well	DNA_Library_set58/set1/G10.png	DNA_Library_set58/set1/H10.png
RIN	9.4	9.5
libSample_RNA_Well	RNA_Library_set58/set1/G4.png	RNA_Library_set58/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-53	BGRSLV03-54
RBP	ZMAT3	ZMAT3
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	3538	3539

Sequencing Information

	BGRSLV03-53	BGRSLV03-54
Sample_ID	BGRSLV03-53	BGRSLV03-54
Sample Name	ZMAT3-BGRSLV03-53	ZMAT3-BGRSLV03-54
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	40,742,510	48,404,253
total_aligned_reads	35,793,917	42,308,936
unique_aligned_reads	33,450,400	39,579,901
percent_uniqueAligned	0.82102	0.81769
correlation_replicates	0.986600	0.986600
spikein_reads	254,126	269,066
percent_spikeins	0.00624	0.00556
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2409	2410

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
ZMAT3-BGRSLV03-53_S165_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2409	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	8156
ZMAT3-BGRSLV03-53_S165_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2409	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	8198
ZMAT3-BGRSLV03-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2409					GRCh38	V40	ZMAT3-BGRSLV03-53_S165_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BGRSLV03-53_S165_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11277
ZMAT3-BGRSLV03-53_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	2409					GRCh38	V40	ZMAT3-BGRSLV03-53/Aligned.sortedByCoord.out.bam		ENCORE2	11319
ZMAT3-BGRSLV03-53_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	2409					GRCh38	V40	ZMAT3-BGRSLV03-53/Aligned.sortedByCoord.out.bam		ENCORE2	11361
ZMAT3-BGRSLV03-53_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	2409					GRCh38	V40	ZMAT3-BGRSLV03-53/Aligned.sortedByCoord.out.bam		ENCORE2	11403
ZMAT3-BGRSLV03-53_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	2409					GRCh38	V40	ZMAT3-BGRSLV03-53/Aligned.sortedByCoord.out.bam		ENCORE2	11445
ZMAT3-BGRSLV03-53_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2409					GRCh38	V40	ZMAT3-BGRSLV03-53_S165_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BGRSLV03-53_S165_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11487
ZMAT3-BGRSLV03-54_S166_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2410	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	8157
ZMAT3-BGRSLV03-54_S166_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2410	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	8199
ZMAT3-BGRSLV03-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2410					GRCh38	V40	ZMAT3-BGRSLV03-54_S166_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BGRSLV03-54_S166_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11278
ZMAT3-BGRSLV03-54_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	2410					GRCh38	V40	ZMAT3-BGRSLV03-54/Aligned.sortedByCoord.out.bam		ENCORE2	11320
ZMAT3-BGRSLV03-54_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	2410					GRCh38	V40	ZMAT3-BGRSLV03-54/Aligned.sortedByCoord.out.bam		ENCORE2	11362
ZMAT3-BGRSLV03-54_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	2410					GRCh38	V40	ZMAT3-BGRSLV03-54/Aligned.sortedByCoord.out.bam		ENCORE2	11404
ZMAT3-BGRSLV03-54_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	2410					GRCh38	V40	ZMAT3-BGRSLV03-54/Aligned.sortedByCoord.out.bam		ENCORE2	11446
ZMAT3-BGRSLV03-54_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2410					GRCh38	V40	ZMAT3-BGRSLV03-54_S166_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BGRSLV03-54_S166_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11488