ZMAT3 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-79	BG293LV06-80
idx	0	0
TRCN#_or_BGC#	TRCN0000128165	TRCN0000128165
shRNA_or_gRNA_sequence	CCGGCATGGTAAGAAACTCCGAAATCTCGAGATTTCGGAGTTTCTTACCATGTTTTTTG	CCGGCATGGTAAGAAACTCCGAAATCTCGAGATTTCGGAGTTTCTTACCATGTTTTTTG
PAM
Name	ZMAT3	ZMAT3
Sample_ID	BG293LV06-79	BG293LV06-80
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	ZMAT3	ZMAT3
qPCR_result	90.4	86.6
Ave_qPCR	88.5
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	12214	12215

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-79	BG293LV06-80
Sample_ID	BG293LV06-79	BG293LV06-80
Sample Name
Sample Name	ZMAT3-BG293LV06-79B	ZMAT3-BG293LV06-80B
RBP	ZMAT3	ZMAT3
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13516	13517

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-79	BG293LV06-80
Sample #	79	80
Sample Name	ZMAT3-BG293LV06-79B	ZMAT3-BG293LV06-80B
Sample_Name_Alias
Index Well Position	G03	H03
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	283	274
Peak_Molarity	61.30	63.50
libSampleQC_DNA_Well	DNA_Library_set72/set1/G3.png	DNA_Library_set72/set1/H3.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set72/set1/G3.png	RNA_Library_set72/set1/H3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-79	BG293LV06-80
RBP	ZMAT3	ZMAT3
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4504	4505

Sequencing Information

	BG293LV06-79	BG293LV06-80
Sample_ID	BG293LV06-79	BG293LV06-80
Sample Name	ZMAT3-BG293LV06-79B	ZMAT3-BG293LV06-80B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	36,343,510	42,345,053
total_aligned_reads	32,414,513	37,944,059
unique_aligned_reads	30,302,739	35,359,439
percent_uniqueAligned	0.83379	0.83503
correlation_replicates	0.993497	0.993497
spikein_reads	126,138	230,818
percent_spikeins	0.00347	0.00545
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3073	3074

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-BG293LV06-79B_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3073	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29832
ZMAT3-BG293LV06-79B_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3073	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29904
ZMAT3-BG293LV06-79B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3073					GRCh38	V40	ZMAT3-BG293LV06-79B_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BG293LV06-79B_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29976
ZMAT3-BG293LV06-79B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3073					GRCh38	V40	ZMAT3-BG293LV06-79B_Aligned.sortedByCoord.out.bam		ENCORE2	30048
ZMAT3-BG293LV06-79B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3073					GRCh38	V40	ZMAT3-BG293LV06-79B_Aligned.sortedByCoord.out.bam		ENCORE2	30120
ZMAT3-BG293LV06-79B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3073					GRCh38	V40	ZMAT3-BG293LV06-79B_Aligned.sortedByCoord.out.bam		ENCORE2	30192
ZMAT3-BG293LV06-79B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3073					GRCh38	V40	ZMAT3-BG293LV06-79B_Aligned.sortedByCoord.out.bam		ENCORE2	30264
ZMAT3-BG293LV06-79B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3073					GRCh38	V40	ZMAT3-BG293LV06-79B_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BG293LV06-79B_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30336
ZMAT3-BG293LV06-80B_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3074	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29833
ZMAT3-BG293LV06-80B_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3074	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29905
ZMAT3-BG293LV06-80B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3074					GRCh38	V40	ZMAT3-BG293LV06-80B_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BG293LV06-80B_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29977
ZMAT3-BG293LV06-80B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3074					GRCh38	V40	ZMAT3-BG293LV06-80B_Aligned.sortedByCoord.out.bam		ENCORE2	30049
ZMAT3-BG293LV06-80B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3074					GRCh38	V40	ZMAT3-BG293LV06-80B_Aligned.sortedByCoord.out.bam		ENCORE2	30121
ZMAT3-BG293LV06-80B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3074					GRCh38	V40	ZMAT3-BG293LV06-80B_Aligned.sortedByCoord.out.bam		ENCORE2	30193
ZMAT3-BG293LV06-80B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3074					GRCh38	V40	ZMAT3-BG293LV06-80B_Aligned.sortedByCoord.out.bam		ENCORE2	30265
ZMAT3-BG293LV06-80B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3074					GRCh38	V40	ZMAT3-BG293LV06-80B_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZMAT3-BG293LV06-80B_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30337