ZCCHC10 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV07-43	BGRSLV07-44
idx	0	0
TRCN#_or_BGC#	TRCN0000134644	TRCN0000134644
shRNA_or_gRNA_sequence	CCGGGCAACATGTAAGATGTCAGAACTCGAGTTCTGACATCTTACATGTTGCTTTTTTG	CCGGGCAACATGTAAGATGTCAGAACTCGAGTTCTGACATCTTACATGTTGCTTTTTTG
PAM
Name	ZCCHC10	ZCCHC10
Sample_ID	BGRSLV07-43	BGRSLV07-44
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	ZCCHC10	ZCCHC10
qPCR_result	76.2	70.4
Ave_qPCR	73.3
RT-qPCR_primer-F	GCCCTCAAGGACAGCAGAACTA
RT-qPCR_primer-R	CTGCTACTGGAACTGGTTACACT
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	8625	8626

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV07-43	BGRSLV07-44
Sample_ID	BGRSLV07-43	BGRSLV07-44
Sample Name
Sample Name	ZCCHC10-BGRSLV07-43	ZCCHC10-BGRSLV07-44
RBP	ZCCHC10	ZCCHC10
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	11852	11853

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV07-43	BGRSLV07-44
Sample #	33	34
Sample Name	ZCCHC10-BGRSLV07-43	ZCCHC10-BGRSLV07-44
Sample_Name_Alias
Index Well Position	A05	B05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	285	295
Peak_Molarity	44.10	60.20
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/A5.png	DNA_Library_set60-62/set4/B5.png
RIN	9.7	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/A5.png	RNA_Library_set60-62/set2/B5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV07-43	BGRSLV07-44
RBP	ZCCHC10	ZCCHC10
Batch_ID	BGRSLV07	BGRSLV07
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3716	3717

Sequencing Information

	BGRSLV07-43	BGRSLV07-44
Sample_ID	BGRSLV07-43	BGRSLV07-44
Sample Name	ZCCHC10-BGRSLV07-43	ZCCHC10-BGRSLV07-44
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	32,832,048	22,434,857
total_aligned_reads	21,503,479	18,067,031
unique_aligned_reads	20,016,458	16,903,226
percent_uniqueAligned	0.60966	0.75344
correlation_replicates	0.964366	0.964366
spikein_reads	83,610	33,302
percent_spikeins	0.00255	0.00148
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2587	2588

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
ZCCHC10-BGRSLV07-43_S33_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2587	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7898
ZCCHC10-BGRSLV07-43_S33_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2587	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7942
ZCCHC10-BGRSLV07-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2587					GRCh38	V40	ZCCHC10-BGRSLV07-43_S33_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC10-BGRSLV07-43_S33_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10203
ZCCHC10-BGRSLV07-43_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2587					GRCh38	V40	ZCCHC10-BGRSLV07-43/Aligned.sortedByCoord.out.bam		ENCORE2	10247
ZCCHC10-BGRSLV07-43_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2587					GRCh38	V40	ZCCHC10-BGRSLV07-43/Aligned.sortedByCoord.out.bam		ENCORE2	10291
ZCCHC10-BGRSLV07-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2587					GRCh38	V40	ZCCHC10-BGRSLV07-43/Aligned.sortedByCoord.out.bam		ENCORE2	10335
ZCCHC10-BGRSLV07-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2587					GRCh38	V40	ZCCHC10-BGRSLV07-43/Aligned.sortedByCoord.out.bam		ENCORE2	10379
ZCCHC10-BGRSLV07-43_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2587					GRCh38	V40	ZCCHC10-BGRSLV07-43_S33_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC10-BGRSLV07-43_S33_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10423
ZCCHC10-BGRSLV07-44_S34_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2588	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7899
ZCCHC10-BGRSLV07-44_S34_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2588	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7943
ZCCHC10-BGRSLV07-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2588					GRCh38	V40	ZCCHC10-BGRSLV07-44_S34_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC10-BGRSLV07-44_S34_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10204
ZCCHC10-BGRSLV07-44_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2588					GRCh38	V40	ZCCHC10-BGRSLV07-44/Aligned.sortedByCoord.out.bam		ENCORE2	10248
ZCCHC10-BGRSLV07-44_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2588					GRCh38	V40	ZCCHC10-BGRSLV07-44/Aligned.sortedByCoord.out.bam		ENCORE2	10292
ZCCHC10-BGRSLV07-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2588					GRCh38	V40	ZCCHC10-BGRSLV07-44/Aligned.sortedByCoord.out.bam		ENCORE2	10336
ZCCHC10-BGRSLV07-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2588					GRCh38	V40	ZCCHC10-BGRSLV07-44/Aligned.sortedByCoord.out.bam		ENCORE2	10380
ZCCHC10-BGRSLV07-44_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2588					GRCh38	V40	ZCCHC10-BGRSLV07-44_S34_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC10-BGRSLV07-44_S34_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10424