ZC3H3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV03-47dox	BGRSDLV03-48dox
idx	0	0
TRCN#_or_BGC#	TRCN0000365519	TRCN0000365519
shRNA_or_gRNA_sequence	CCGGGAACGTGGTCATCAAAGTTAACTCGAGTTAACTTTGATGACCACGTTCTTTTTG	CCGGGAACGTGGTCATCAAAGTTAACTCGAGTTAACTTTGATGACCACGTTCTTTTTG
PAM
Name	ZC3H3	ZC3H3
Sample_ID	BGRSDLV03-47dox	BGRSDLV03-48dox
transduction_Date	9/29/23	9/29/23
days	4 days	4 days
RBP_name	ZC3H3	ZC3H3
qPCR_result	61.5	67.5
Ave_qPCR	64.5
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	9361	9362

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV03-47dox	BGRSDLV03-48dox
Sample_ID	BGRSDLV03-47dox	BGRSDLV03-48dox
Sample Name
Sample Name	ZC3H3-BGRSDLV03-47dox	ZC3H3-BGRSDLV03-48dox
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	12636	12637

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV03-47dox	BGRSDLV03-48dox
Sample #	39	40
Sample Name	ZC3H3-BGRSDLV03-47dox	ZC3H3-BGRSDLV03-48dox
Sample_Name_Alias
Index Well Position	G09	H09
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	273	275
Peak_Molarity	51.60	41.00
libSampleQC_DNA_Well	DNA_Library_set66/set1/G10.png	DNA_Library_set66/set1/H10.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set66/set1/G5.png	RNA_Library_set66/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-18	2023-10-18
Sample_ID	BGRSDLV03-47dox	BGRSDLV03-48dox
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	4072	4073

Sequencing Information

	BGRSDLV03-47dox	BGRSDLV03-48dox
Sample_ID	BGRSDLV03-47dox	BGRSDLV03-48dox
Sample Name	ZC3H3-BGRSDLV03-47dox	ZC3H3-BGRSDLV03-48dox
Pool ID	Pool-231018	Pool-231018
LocalServer_folder	set66	set66
total_reads	17,746,503	19,351,195
total_aligned_reads	15,832,347	16,956,360
unique_aligned_reads	14,809,795	15,815,945
percent_uniqueAligned	0.83452	0.81731
correlation_replicates	0.994322	0.994322
spikein_reads	3,418	7,408
percent_spikeins	0.00019	0.00038
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2791	2792

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-BGRSDLV03-47dox_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2791	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8944
ZC3H3-BGRSDLV03-47dox_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2791	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8984
ZC3H3-BGRSDLV03-47dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2791					GRCh38	V40	ZC3H3-BGRSDLV03-47dox_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSDLV03-47dox_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9024
ZC3H3-BGRSDLV03-47dox_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	2791					GRCh38	V40	ZC3H3-BGRSDLV03-47dox/Aligned.sortedByCoord.out.bam		ENCORE2	9064
ZC3H3-BGRSDLV03-47dox_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	2791					GRCh38	V40	ZC3H3-BGRSDLV03-47dox/Aligned.sortedByCoord.out.bam		ENCORE2	9104
ZC3H3-BGRSDLV03-47dox_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	2791					GRCh38	V40	ZC3H3-BGRSDLV03-47dox/Aligned.sortedByCoord.out.bam		ENCORE2	9144
ZC3H3-BGRSDLV03-47dox_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	2791					GRCh38	V40	ZC3H3-BGRSDLV03-47dox/Aligned.sortedByCoord.out.bam		ENCORE2	9184
ZC3H3-BGRSDLV03-47dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2791					GRCh38	V40	ZC3H3-BGRSDLV03-47dox_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSDLV03-47dox_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9224
ZC3H3-BGRSDLV03-48dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2792	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV03-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8945
ZC3H3-BGRSDLV03-48dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set66/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2792	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV03-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV03-4dox_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8985
ZC3H3-BGRSDLV03-48dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set66/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2792					GRCh38	V40	ZC3H3-BGRSDLV03-48dox_merged_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSDLV03-48dox_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9025
ZC3H3-BGRSDLV03-48dox_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	2792					GRCh38	V40	ZC3H3-BGRSDLV03-48dox/Aligned.sortedByCoord.out.bam		ENCORE2	9065
ZC3H3-BGRSDLV03-48dox_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	2792					GRCh38	V40	ZC3H3-BGRSDLV03-48dox/Aligned.sortedByCoord.out.bam		ENCORE2	9105
ZC3H3-BGRSDLV03-48dox_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	2792					GRCh38	V40	ZC3H3-BGRSDLV03-48dox/Aligned.sortedByCoord.out.bam		ENCORE2	9145
ZC3H3-BGRSDLV03-48dox_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	2792					GRCh38	V40	ZC3H3-BGRSDLV03-48dox/Aligned.sortedByCoord.out.bam		ENCORE2	9185
ZC3H3-BGRSDLV03-48dox_quant.sf	ENCODE_DATA/set66/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2792					GRCh38	V40	ZC3H3-BGRSDLV03-48dox_merged_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSDLV03-48dox_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9225