ZC3H18 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-65	BGRSLV02-66
idx	0	0
TRCN#_or_BGC#	TRCN0000075169	TRCN0000075169
shRNA_or_gRNA_sequence	CCGGCGCAGACCCTTATTATGACTACTCGAGTAGTCATAATAAGGGTCTGCGTTTTTG	CCGGCGCAGACCCTTATTATGACTACTCGAGTAGTCATAATAAGGGTCTGCGTTTTTG
PAM
Name	ZC3H18	ZC3H18
Sample_ID	BGRSLV02-65	BGRSLV02-66
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	ZC3H18	ZC3H18
qPCR_result	78.2	62.3
Ave_qPCR	70.2
RT-qPCR_primer-F	gcgctatgaaccatcagaca
RT-qPCR_primer-R	cagtctcccacctgacttcc
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	8302	8303

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-65	BGRSLV02-66
Sample_ID	BGRSLV02-65	BGRSLV02-66
Sample Name
Sample Name	ZC3H18-BGRSLV02-65	ZC3H18-BGRSLV02-66
RBP	ZC3H18	ZC3H18
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	11340	11341

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-65	BGRSLV02-66
Sample #	43	44
Sample Name	ZC3H18-BGRSLV02-65	ZC3H18-BGRSLV02-66
Sample_Name_Alias
Index Well Position	C06	D06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	299	298
Peak_Molarity	72.90	53.80
libSampleQC_DNA_Well	DNA_Library_set57/set1/C12.png	DNA_Library_set57/set1/D12.png
RIN	9.0	9.7
libSample_RNA_Well	RNA_Library_set57/set1/C6.png	RNA_Library_set57/set1/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-65	BGRSLV02-66
RBP	ZC3H18	ZC3H18
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3504	3505

Sequencing Information

	BGRSLV02-65	BGRSLV02-66
Sample_ID	BGRSLV02-65	BGRSLV02-66
Sample Name	ZC3H18-BGRSLV02-65	ZC3H18-BGRSLV02-66
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	36,242,899	39,591,096
total_aligned_reads	33,882,240	36,994,383
unique_aligned_reads	31,588,334	34,544,716
percent_uniqueAligned	0.87157	0.87254
correlation_replicates	0.993125	0.993125
spikein_reads	21,036	20,488
percent_spikeins	0.00058	0.00052
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2375	2376

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
ZC3H18-BGRSLV02-65_S131_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2375	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8238
ZC3H18-BGRSLV02-65_S131_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2375	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8284
ZC3H18-BGRSLV02-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2375					GRCh38	V40	ZC3H18-BGRSLV02-65_S131_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H18-BGRSLV02-65_S131_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11527
ZC3H18-BGRSLV02-65_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2375					GRCh38	V40	ZC3H18-BGRSLV02-65/Aligned.sortedByCoord.out.bam		ENCORE2	11573
ZC3H18-BGRSLV02-65_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2375					GRCh38	V40	ZC3H18-BGRSLV02-65/Aligned.sortedByCoord.out.bam		ENCORE2	11619
ZC3H18-BGRSLV02-65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2375					GRCh38	V40	ZC3H18-BGRSLV02-65/Aligned.sortedByCoord.out.bam		ENCORE2	11665
ZC3H18-BGRSLV02-65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2375					GRCh38	V40	ZC3H18-BGRSLV02-65/Aligned.sortedByCoord.out.bam		ENCORE2	11711
ZC3H18-BGRSLV02-65_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2375					GRCh38	V40	ZC3H18-BGRSLV02-65_S131_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H18-BGRSLV02-65_S131_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11757
ZC3H18-BGRSLV02-66_S132_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2376	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8239
ZC3H18-BGRSLV02-66_S132_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2376	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8285
ZC3H18-BGRSLV02-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2376					GRCh38	V40	ZC3H18-BGRSLV02-66_S132_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H18-BGRSLV02-66_S132_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11528
ZC3H18-BGRSLV02-66_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2376					GRCh38	V40	ZC3H18-BGRSLV02-66/Aligned.sortedByCoord.out.bam		ENCORE2	11574
ZC3H18-BGRSLV02-66_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2376					GRCh38	V40	ZC3H18-BGRSLV02-66/Aligned.sortedByCoord.out.bam		ENCORE2	11620
ZC3H18-BGRSLV02-66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2376					GRCh38	V40	ZC3H18-BGRSLV02-66/Aligned.sortedByCoord.out.bam		ENCORE2	11666
ZC3H18-BGRSLV02-66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2376					GRCh38	V40	ZC3H18-BGRSLV02-66/Aligned.sortedByCoord.out.bam		ENCORE2	11712
ZC3H18-BGRSLV02-66_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2376					GRCh38	V40	ZC3H18-BGRSLV02-66_S132_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H18-BGRSLV02-66_S132_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11758