ZC3H3 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-49	BGRSLV03-50
idx	0	0
TRCN#_or_BGC#	TRCN0000365519	TRCN0000365519
shRNA_or_gRNA_sequence	CCGGGAACGTGGTCATCAAAGTTAACTCGAGTTAACTTTGATGACCACGTTCTTTTTG	CCGGGAACGTGGTCATCAAAGTTAACTCGAGTTAACTTTGATGACCACGTTCTTTTTG
PAM
Name	ZC3H3	ZC3H3
Sample_ID	BGRSLV03-49	BGRSLV03-50
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	ZC3H3	ZC3H3
qPCR_result	53.8	59.0
Ave_qPCR	56.4
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	8359	8360

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-49	BGRSLV03-50
Sample_ID	BGRSLV03-49	BGRSLV03-50
Sample Name
Sample Name	ZC3H3-BGRSLV03-49	ZC3H3-BGRSLV03-50
RBP	ZC3H3	ZC3H3
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	11396	11397

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-49	BGRSLV03-50
Sample #	27	28
Sample Name	ZC3H3-BGRSLV03-49	ZC3H3-BGRSLV03-50
Sample_Name_Alias
Index Well Position	C10	D10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	292	290
Peak_Molarity	98.30	119.00
libSampleQC_DNA_Well	DNA_Library_set58/set1/C10.png	DNA_Library_set58/set1/D10.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set58/set1/C4.png	RNA_Library_set58/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-49	BGRSLV03-50
RBP	ZC3H3	ZC3H3
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3534	3535

Sequencing Information

	BGRSLV03-49	BGRSLV03-50
Sample_ID	BGRSLV03-49	BGRSLV03-50
Sample Name	ZC3H3-BGRSLV03-49	ZC3H3-BGRSLV03-50
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	46,713,650	38,480,099
total_aligned_reads	43,058,094	34,639,402
unique_aligned_reads	40,291,927	32,436,819
percent_uniqueAligned	0.86253	0.84295
correlation_replicates	0.998741	0.998741
spikein_reads	313,730	232,190
percent_spikeins	0.00672	0.00603
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2405	2406

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-BGRSLV03-49_S161_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2405	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8152
ZC3H3-BGRSLV03-49_S161_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2405	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8194
ZC3H3-BGRSLV03-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2405					GRCh38	V40	ZC3H3-BGRSLV03-49_S161_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSLV03-49_S161_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11273
ZC3H3-BGRSLV03-49_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2405					GRCh38	V40	ZC3H3-BGRSLV03-49/Aligned.sortedByCoord.out.bam		ENCORE2	11315
ZC3H3-BGRSLV03-49_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2405					GRCh38	V40	ZC3H3-BGRSLV03-49/Aligned.sortedByCoord.out.bam		ENCORE2	11357
ZC3H3-BGRSLV03-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2405					GRCh38	V40	ZC3H3-BGRSLV03-49/Aligned.sortedByCoord.out.bam		ENCORE2	11399
ZC3H3-BGRSLV03-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2405					GRCh38	V40	ZC3H3-BGRSLV03-49/Aligned.sortedByCoord.out.bam		ENCORE2	11441
ZC3H3-BGRSLV03-49_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2405					GRCh38	V40	ZC3H3-BGRSLV03-49_S161_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSLV03-49_S161_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11483
ZC3H3-BGRSLV03-50_S162_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2406	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8153
ZC3H3-BGRSLV03-50_S162_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2406	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8195
ZC3H3-BGRSLV03-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2406					GRCh38	V40	ZC3H3-BGRSLV03-50_S162_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSLV03-50_S162_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11274
ZC3H3-BGRSLV03-50_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2406					GRCh38	V40	ZC3H3-BGRSLV03-50/Aligned.sortedByCoord.out.bam		ENCORE2	11316
ZC3H3-BGRSLV03-50_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2406					GRCh38	V40	ZC3H3-BGRSLV03-50/Aligned.sortedByCoord.out.bam		ENCORE2	11358
ZC3H3-BGRSLV03-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2406					GRCh38	V40	ZC3H3-BGRSLV03-50/Aligned.sortedByCoord.out.bam		ENCORE2	11400
ZC3H3-BGRSLV03-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2406					GRCh38	V40	ZC3H3-BGRSLV03-50/Aligned.sortedByCoord.out.bam		ENCORE2	11442
ZC3H3-BGRSLV03-50_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2406					GRCh38	V40	ZC3H3-BGRSLV03-50_S162_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H3-BGRSLV03-50_S162_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11484