ZC3H3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-45	BGRSDLV03-46
idx	0	0
TRCN#_or_BGC#	TRCN0000365519	TRCN0000365519
shRNA_or_gRNA_sequence	CCGGGAACGTGGTCATCAAAGTTAACTCGAGTTAACTTTGATGACCACGTTCTTTTTG	CCGGGAACGTGGTCATCAAAGTTAACTCGAGTTAACTTTGATGACCACGTTCTTTTTG
PAM
Name	ZC3H3	ZC3H3
Sample_ID	BGRSDLV03-45	BGRSDLV03-46
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	ZC3H3	ZC3H3
qPCR_result	62.5	61.7
Ave_qPCR	62.1
RT-qPCR_primer-F	GTAGGACACAGTGGCTTGAAGC
RT-qPCR_primer-R	GTGCCGCTTTTCTTGTCTCCAG
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	9359	9360

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-45	BGRSDLV03-46
Sample_ID	BGRSDLV03-45	BGRSDLV03-46
Sample Name
Sample Name	ZC3H3-BGRSDLV03-45	ZC3H3-BGRSDLV03-46
RBP	ZC3H3	ZC3H3
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12634	12635

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-45	BGRSDLV03-46
Sample #	37	38
Sample Name	ZC3H3-BGRSDLV03-45	ZC3H3-BGRSDLV03-46
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-17	2023-10-17
Lib_ID	Lib-231017	Lib-231017
Tecan_Location
Tecan
Tecan_date
Size_bp	278	279
Peak_Molarity	60.80	67.50
libSampleQC_DNA_Well	DNA_Library_set66/set1/E10.png	DNA_Library_set66/set1/F10.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set66/set1/E5.png	RNA_Library_set66/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-45	BGRSDLV03-46
RBP	ZC3H3	ZC3H3
Batch_ID	BGRSDLV03	BGRSDLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4070	4071

Sequencing Information

	BGRSDLV03-45	BGRSDLV03-46
Sample_ID	BGRSDLV03-45	BGRSDLV03-46
Sample Name	ZC3H3-BGRSDLV03-45	ZC3H3-BGRSDLV03-46
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	13,616,079	15,330,157
total_aligned_reads	12,058,237	13,644,863
unique_aligned_reads	11,261,832	12,714,092
percent_uniqueAligned	0.82710	0.82935
correlation_replicates	0.997190	0.997190
spikein_reads	1,236	1,638
percent_spikeins	0.00009	0.00011
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2789	2790

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
ZC3H3-BGRSDLV03-45_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2789	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8942
ZC3H3-BGRSDLV03-45_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2789	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8982
ZC3H3-BGRSDLV03-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2789					GRCh38	V40	ZC3H3-BGRSDLV03-45_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSDLV03-45_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9022
ZC3H3-BGRSDLV03-45_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2789					GRCh38	V40	ZC3H3-BGRSDLV03-45/Aligned.sortedByCoord.out.bam		ENCORE2	9062
ZC3H3-BGRSDLV03-45_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2789					GRCh38	V40	ZC3H3-BGRSDLV03-45/Aligned.sortedByCoord.out.bam		ENCORE2	9102
ZC3H3-BGRSDLV03-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2789					GRCh38	V40	ZC3H3-BGRSDLV03-45/Aligned.sortedByCoord.out.bam		ENCORE2	9142
ZC3H3-BGRSDLV03-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2789					GRCh38	V40	ZC3H3-BGRSDLV03-45/Aligned.sortedByCoord.out.bam		ENCORE2	9182
ZC3H3-BGRSDLV03-45_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2789					GRCh38	V40	ZC3H3-BGRSDLV03-45_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSDLV03-45_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9222
ZC3H3-BGRSDLV03-46_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2790	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8943
ZC3H3-BGRSDLV03-46_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2790	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-2_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8983
ZC3H3-BGRSDLV03-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2790					GRCh38	V40	ZC3H3-BGRSDLV03-46_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSDLV03-46_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9023
ZC3H3-BGRSDLV03-46_Signal.Unique.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2790					GRCh38	V40	ZC3H3-BGRSDLV03-46/Aligned.sortedByCoord.out.bam		ENCORE2	9063
ZC3H3-BGRSDLV03-46_Signal.Unique.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2790					GRCh38	V40	ZC3H3-BGRSDLV03-46/Aligned.sortedByCoord.out.bam		ENCORE2	9103
ZC3H3-BGRSDLV03-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2790					GRCh38	V40	ZC3H3-BGRSDLV03-46/Aligned.sortedByCoord.out.bam		ENCORE2	9143
ZC3H3-BGRSDLV03-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2790					GRCh38	V40	ZC3H3-BGRSDLV03-46/Aligned.sortedByCoord.out.bam		ENCORE2	9183
ZC3H3-BGRSDLV03-46_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2790					GRCh38	V40	ZC3H3-BGRSDLV03-46_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSDLV03-46_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9223