ZCCHC7 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-51	BGRSLV02-52
idx	0	0
TRCN#_or_BGC#	TRCN0000033990	TRCN0000033990
shRNA_or_gRNA_sequence	CCGGCCACACGTCAAGAGAAGACAACTCGAGTTGTCTTCTCTTGACGTGTGGTTTTTG	CCGGCCACACGTCAAGAGAAGACAACTCGAGTTGTCTTCTCTTGACGTGTGGTTTTTG
PAM
Name	ZCCHC7	ZCCHC7
Sample_ID	BGRSLV02-51	BGRSLV02-52
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	ZCCHC7	ZCCHC7
qPCR_result	72.0	56.5
Ave_qPCR	64.2
RT-qPCR_primer-F	CCTGTGCCTAAGATGTTGGACC
RT-qPCR_primer-R	GCCTCCAGATTTCTGTGCAAGC
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	8288	8289

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-51	BGRSLV02-52
Sample_ID	BGRSLV02-51	BGRSLV02-52
Sample Name
Sample Name	ZCCHC7-BGRSLV02-51	ZCCHC7-BGRSLV02-52
RBP	ZCCHC7	ZCCHC7
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	11336	11337

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-51	BGRSLV02-52
Sample #	39	40
Sample Name	ZCCHC7-BGRSLV02-51	ZCCHC7-BGRSLV02-52
Sample_Name_Alias
Index Well Position	G05	H05
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	298	289
Peak_Molarity	31.10	49.00
libSampleQC_DNA_Well	DNA_Library_set57/set1/G11.png	DNA_Library_set57/set1/H11.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set57/set1/G5.png	RNA_Library_set57/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-51	BGRSLV02-52
RBP	ZCCHC7	ZCCHC7
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	3500	3501

Sequencing Information

	BGRSLV02-51	BGRSLV02-52
Sample_ID	BGRSLV02-51	BGRSLV02-52
Sample Name	ZCCHC7-BGRSLV02-51	ZCCHC7-BGRSLV02-52
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	73,181,054	44,092,217
total_aligned_reads	66,027,258	36,021,238
unique_aligned_reads	61,580,034	33,375,627
percent_uniqueAligned	0.84148	0.75695
correlation_replicates	0.982703	0.982703
spikein_reads	48,236	34,152
percent_spikeins	0.00066	0.00077
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2371	2372

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
ZCCHC7-BGRSLV02-51_S127_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2371	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	8242
ZCCHC7-BGRSLV02-51_S127_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2371	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	8288
ZCCHC7-BGRSLV02-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2371					GRCh38	V40	ZCCHC7-BGRSLV02-51_S127_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC7-BGRSLV02-51_S127_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11531
ZCCHC7-BGRSLV02-51_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	2371					GRCh38	V40	ZCCHC7-BGRSLV02-51/Aligned.sortedByCoord.out.bam		ENCORE2	11577
ZCCHC7-BGRSLV02-51_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	2371					GRCh38	V40	ZCCHC7-BGRSLV02-51/Aligned.sortedByCoord.out.bam		ENCORE2	11623
ZCCHC7-BGRSLV02-51_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	2371					GRCh38	V40	ZCCHC7-BGRSLV02-51/Aligned.sortedByCoord.out.bam		ENCORE2	11669
ZCCHC7-BGRSLV02-51_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	2371					GRCh38	V40	ZCCHC7-BGRSLV02-51/Aligned.sortedByCoord.out.bam		ENCORE2	11715
ZCCHC7-BGRSLV02-51_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2371					GRCh38	V40	ZCCHC7-BGRSLV02-51_S127_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC7-BGRSLV02-51_S127_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11761
ZCCHC7-BGRSLV02-52_S128_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2372	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	8243
ZCCHC7-BGRSLV02-52_S128_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2372	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	8289
ZCCHC7-BGRSLV02-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2372					GRCh38	V40	ZCCHC7-BGRSLV02-52_S128_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC7-BGRSLV02-52_S128_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11532
ZCCHC7-BGRSLV02-52_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	2372					GRCh38	V40	ZCCHC7-BGRSLV02-52/Aligned.sortedByCoord.out.bam		ENCORE2	11578
ZCCHC7-BGRSLV02-52_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	2372					GRCh38	V40	ZCCHC7-BGRSLV02-52/Aligned.sortedByCoord.out.bam		ENCORE2	11624
ZCCHC7-BGRSLV02-52_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	2372					GRCh38	V40	ZCCHC7-BGRSLV02-52/Aligned.sortedByCoord.out.bam		ENCORE2	11670
ZCCHC7-BGRSLV02-52_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	2372					GRCh38	V40	ZCCHC7-BGRSLV02-52/Aligned.sortedByCoord.out.bam		ENCORE2	11716
ZCCHC7-BGRSLV02-52_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2372					GRCh38	V40	ZCCHC7-BGRSLV02-52_S128_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZCCHC7-BGRSLV02-52_S128_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11762