ZC3HC1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-65	BGRSLV04-66
idx	0	0
TRCN#_or_BGC#	TRCN0000037541	TRCN0000037541
shRNA_or_gRNA_sequence	CCGGCTCTCTGAGAAATCAAGGAAACTCGAGTTTCCTTGATTTCTCAGAGAGTTTTTG	CCGGCTCTCTGAGAAATCAAGGAAACTCGAGTTTCCTTGATTTCTCAGAGAGTTTTTG
PAM
Name	ZC3HC1	ZC3HC1
Sample_ID	BGRSLV04-65	BGRSLV04-66
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	ZC3HC1	ZC3HC1
qPCR_result	76.0	84.3
Ave_qPCR	80.2
RT-qPCR_primer-F	gccggaggacttgaaaacta
RT-qPCR_primer-R	cagtgacgtggacttggatg
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	8445	8446

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-65	BGRSLV04-66
Sample_ID	BGRSLV04-65	BGRSLV04-66
Sample Name
Sample Name	ZC3HC1-BGRSLV04-65	ZC3HC1-BGRSLV04-66
RBP	ZC3HC1	ZC3HC1
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	11472	11473

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-65	BGRSLV04-66
Sample #	37	38
Sample Name	ZC3HC1-BGRSLV04-65	ZC3HC1-BGRSLV04-66
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-03-02	2023-03-02
Lib_ID	Lib-230302	Lib-230302
Tecan_Location
Tecan
Tecan_date
Size_bp	274	286
Peak_Molarity	63.00	61.30
libSampleQC_DNA_Well	DNA_Library_set59/set1/E11.png	DNA_Library_set59/set1/F11.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set59/set1/E6.png	RNA_Library_set59/set1/F6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-65	BGRSLV04-66
RBP	ZC3HC1	ZC3HC1
Batch_ID	BGRSLV04	BGRSLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3586	3587

Sequencing Information

	BGRSLV04-65	BGRSLV04-66
Sample_ID	BGRSLV04-65	BGRSLV04-66
Sample Name	ZC3HC1-BGRSLV04-65	ZC3HC1-BGRSLV04-66
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	76,732,504	77,315,755
total_aligned_reads	63,891,296	65,236,660
unique_aligned_reads	59,017,614	60,358,208
percent_uniqueAligned	0.76913	0.78067
correlation_replicates	0.988131	0.988131
spikein_reads	198,530	221,694
percent_spikeins	0.00259	0.00287
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2457	2458

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
ZC3HC1-BGRSLV04-65_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2457	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8086
ZC3HC1-BGRSLV04-65_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2457	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8124
ZC3HC1-BGRSLV04-65_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2457					GRCh38	V40	ZC3HC1-BGRSLV04-65_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HC1-BGRSLV04-65_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11055
ZC3HC1-BGRSLV04-65_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2457					GRCh38	V40	ZC3HC1-BGRSLV04-65/Aligned.sortedByCoord.out.bam		ENCORE2	11093
ZC3HC1-BGRSLV04-65_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2457					GRCh38	V40	ZC3HC1-BGRSLV04-65/Aligned.sortedByCoord.out.bam		ENCORE2	11131
ZC3HC1-BGRSLV04-65_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2457					GRCh38	V40	ZC3HC1-BGRSLV04-65/Aligned.sortedByCoord.out.bam		ENCORE2	11169
ZC3HC1-BGRSLV04-65_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2457					GRCh38	V40	ZC3HC1-BGRSLV04-65/Aligned.sortedByCoord.out.bam		ENCORE2	11207
ZC3HC1-BGRSLV04-65_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2457					GRCh38	V40	ZC3HC1-BGRSLV04-65_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HC1-BGRSLV04-65_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11245
ZC3HC1-BGRSLV04-66_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2458	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8087
ZC3HC1-BGRSLV04-66_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2458	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8125
ZC3HC1-BGRSLV04-66_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2458					GRCh38	V40	ZC3HC1-BGRSLV04-66_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HC1-BGRSLV04-66_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11056
ZC3HC1-BGRSLV04-66_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2458					GRCh38	V40	ZC3HC1-BGRSLV04-66/Aligned.sortedByCoord.out.bam		ENCORE2	11094
ZC3HC1-BGRSLV04-66_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2458					GRCh38	V40	ZC3HC1-BGRSLV04-66/Aligned.sortedByCoord.out.bam		ENCORE2	11132
ZC3HC1-BGRSLV04-66_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2458					GRCh38	V40	ZC3HC1-BGRSLV04-66/Aligned.sortedByCoord.out.bam		ENCORE2	11170
ZC3HC1-BGRSLV04-66_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2458					GRCh38	V40	ZC3HC1-BGRSLV04-66/Aligned.sortedByCoord.out.bam		ENCORE2	11208
ZC3HC1-BGRSLV04-66_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2458					GRCh38	V40	ZC3HC1-BGRSLV04-66_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,ZC3HC1-BGRSLV04-66_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11246