ZC3H7A RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV08-7	BGRSLV08-8
idx	0	0
TRCN#_or_BGC#	TRCN0000161104	TRCN0000161104
shRNA_or_gRNA_sequence	CCGGGCGATGAGAGTGATGTCTATTCTCGAGAATAGACATCACTCTCATCGCTTTTTTG	CCGGGCGATGAGAGTGATGTCTATTCTCGAGAATAGACATCACTCTCATCGCTTTTTTG
PAM
Name	ZC3H7A	ZC3H7A
Sample_ID	BGRSLV08-7	BGRSLV08-8
transduction_Date	4/22/23	4/22/23
days	D4	D4
RBP_name	ZC3H7A	ZC3H7A
qPCR_result	83.5	81.9
Ave_qPCR	82.7
RT-qPCR_primer-F	agtgcaaaagcaaggcattc
RT-qPCR_primer-R	tgtttctttgtggggagagg
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	8656	8657

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV08-7	BGRSLV08-8
Sample_ID	BGRSLV08-7	BGRSLV08-8
Sample Name
Sample Name	ZC3H7A-BGRSLV08-7	ZC3H7A-BGRSLV08-8
RBP	ZC3H7A	ZC3H7A
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	11780	11781

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV08-7	BGRSLV08-8
Sample #	45	46
Sample Name	ZC3H7A-BGRSLV08-7	ZC3H7A-BGRSLV08-8
Sample_Name_Alias
Index Well Position	E06	F06
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	303	301
Peak_Molarity	99.40	78.50
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/E6.png	DNA_Library_set60-62/set4/F6.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set60-62/set2/E6.png	RNA_Library_set60-62/set2/F6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV08-7	BGRSLV08-8
RBP	ZC3H7A	ZC3H7A
Batch_ID	BGRSLV08	BGRSLV08
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3728	3729

Sequencing Information

	BGRSLV08-7	BGRSLV08-8
Sample_ID	BGRSLV08-7	BGRSLV08-8
Sample Name	ZC3H7A-BGRSLV08-7	ZC3H7A-BGRSLV08-8
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	28,818,608	25,919,164
total_aligned_reads	24,278,187	21,995,200
unique_aligned_reads	22,750,597	20,659,212
percent_uniqueAligned	0.78944	0.79706
correlation_replicates	0.990475	0.990475
spikein_reads	24,166	17,802
percent_spikeins	0.00084	0.00069
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2599	2600

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
ZC3H7A-BGRSLV08-7_S45_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2599	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7896
ZC3H7A-BGRSLV08-7_S45_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2599	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7940
ZC3H7A-BGRSLV08-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2599					GRCh38	V40	ZC3H7A-BGRSLV08-7_S45_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H7A-BGRSLV08-7_S45_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10201
ZC3H7A-BGRSLV08-7_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	2599					GRCh38	V40	ZC3H7A-BGRSLV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	10245
ZC3H7A-BGRSLV08-7_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	2599					GRCh38	V40	ZC3H7A-BGRSLV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	10289
ZC3H7A-BGRSLV08-7_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	2599					GRCh38	V40	ZC3H7A-BGRSLV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	10333
ZC3H7A-BGRSLV08-7_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	2599					GRCh38	V40	ZC3H7A-BGRSLV08-7/Aligned.sortedByCoord.out.bam		ENCORE2	10377
ZC3H7A-BGRSLV08-7_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2599					GRCh38	V40	ZC3H7A-BGRSLV08-7_S45_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H7A-BGRSLV08-7_S45_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10421
ZC3H7A-BGRSLV08-8_S46_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2600	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7897
ZC3H7A-BGRSLV08-8_S46_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2600	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7941
ZC3H7A-BGRSLV08-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2600					GRCh38	V40	ZC3H7A-BGRSLV08-8_S46_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H7A-BGRSLV08-8_S46_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10202
ZC3H7A-BGRSLV08-8_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	2600					GRCh38	V40	ZC3H7A-BGRSLV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	10246
ZC3H7A-BGRSLV08-8_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	2600					GRCh38	V40	ZC3H7A-BGRSLV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	10290
ZC3H7A-BGRSLV08-8_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	2600					GRCh38	V40	ZC3H7A-BGRSLV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	10334
ZC3H7A-BGRSLV08-8_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	2600					GRCh38	V40	ZC3H7A-BGRSLV08-8/Aligned.sortedByCoord.out.bam		ENCORE2	10378
ZC3H7A-BGRSLV08-8_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2600					GRCh38	V40	ZC3H7A-BGRSLV08-8_S46_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZC3H7A-BGRSLV08-8_S46_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10422