ZC3H8 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-19	BGRSLV02-20
idx	0	0
TRCN#_or_BGC#	TRCN0000163082	TRCN0000163082
shRNA_or_gRNA_sequence	CCGGGCAGCATTTGAGTCAGGCATTCTCGAGAATGCCTGACTCAAATGCTGCTTTTTTG	CCGGGCAGCATTTGAGTCAGGCATTCTCGAGAATGCCTGACTCAAATGCTGCTTTTTTG
PAM
Name	ZC3H8	ZC3H8
Sample_ID	BGRSLV02-19	BGRSLV02-20
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	ZC3H8	ZC3H8
qPCR_result	59.4	70.3
Ave_qPCR	64.8
RT-qPCR_primer-F	ttttggatactgaaaagaagtcatgt
RT-qPCR_primer-R	acagtcttgaacacgcatgg
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	8256	8257

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-19	BGRSLV02-20
Sample_ID	BGRSLV02-19	BGRSLV02-20
Sample Name
Sample Name	ZC3H8-BGRSLV02-19	ZC3H8-BGRSLV02-20
RBP	ZC3H8	ZC3H8
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	11306	11307

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-19	BGRSLV02-20
Sample #	9	10
Sample Name	ZC3H8-BGRSLV02-19	ZC3H8-BGRSLV02-20
Sample_Name_Alias
Index Well Position	A02	B02
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	290	289
Peak_Molarity	52.40	43.30
libSampleQC_DNA_Well	DNA_Library_set57/set1/A8.png	DNA_Library_set57/set1/B8.png
RIN	10.0	9.8
libSample_RNA_Well	RNA_Library_set57/set1/A2.png	RNA_Library_set57/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-19	BGRSLV02-20
RBP	ZC3H8	ZC3H8
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	3470	3471

Sequencing Information

	BGRSLV02-19	BGRSLV02-20
Sample_ID	BGRSLV02-19	BGRSLV02-20
Sample Name	ZC3H8-BGRSLV02-19	ZC3H8-BGRSLV02-20
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	45,958,961	55,927,550
total_aligned_reads	42,005,454	50,683,282
unique_aligned_reads	39,091,270	47,467,741
percent_uniqueAligned	0.85057	0.84874
correlation_replicates	0.995792	0.995792
spikein_reads	27,304	32,584
percent_spikeins	0.00059	0.00058
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2341	2342

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
ZC3H8-BGRSLV02-19_S97_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2341	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	8240
ZC3H8-BGRSLV02-19_S97_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2341	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	8286
ZC3H8-BGRSLV02-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2341					GRCh38	V40	ZC3H8-BGRSLV02-19_S97_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H8-BGRSLV02-19_S97_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11529
ZC3H8-BGRSLV02-19_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	2341					GRCh38	V40	ZC3H8-BGRSLV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	11575
ZC3H8-BGRSLV02-19_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	2341					GRCh38	V40	ZC3H8-BGRSLV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	11621
ZC3H8-BGRSLV02-19_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	2341					GRCh38	V40	ZC3H8-BGRSLV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	11667
ZC3H8-BGRSLV02-19_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	2341					GRCh38	V40	ZC3H8-BGRSLV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	11713
ZC3H8-BGRSLV02-19_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2341					GRCh38	V40	ZC3H8-BGRSLV02-19_S97_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H8-BGRSLV02-19_S97_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11759
ZC3H8-BGRSLV02-20_S98_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2342	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	8241
ZC3H8-BGRSLV02-20_S98_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2342	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	8287
ZC3H8-BGRSLV02-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2342					GRCh38	V40	ZC3H8-BGRSLV02-20_S98_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H8-BGRSLV02-20_S98_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11530
ZC3H8-BGRSLV02-20_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	2342					GRCh38	V40	ZC3H8-BGRSLV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	11576
ZC3H8-BGRSLV02-20_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	2342					GRCh38	V40	ZC3H8-BGRSLV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	11622
ZC3H8-BGRSLV02-20_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	2342					GRCh38	V40	ZC3H8-BGRSLV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	11668
ZC3H8-BGRSLV02-20_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	2342					GRCh38	V40	ZC3H8-BGRSLV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	11714
ZC3H8-BGRSLV02-20_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2342					GRCh38	V40	ZC3H8-BGRSLV02-20_S98_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H8-BGRSLV02-20_S98_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11760