KDM5A RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-13	BGRSLV04-14
idx	0	0
TRCN#_or_BGC#	TRCN0000014629	TRCN0000014629
shRNA_or_gRNA_sequence	CCGGCCAGACTTACAGGGACACTTACTCGAGTAAGTGTCCCTGTAAGTCTGGTTTTT	CCGGCCAGACTTACAGGGACACTTACTCGAGTAAGTGTCCCTGTAAGTCTGGTTTTT
PAM
Name	KDM5A	KDM5A
Sample_ID	BGRSLV04-13	BGRSLV04-14
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	KDM5A	KDM5A
qPCR_result	52.3	75.7
Ave_qPCR	64.0
RT-qPCR_primer-F	tgaacattctgccgaagaga
RT-qPCR_primer-R	cttttgttcccattgccaag
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	8393	8394

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-13	BGRSLV04-14
Sample_ID	BGRSLV04-13	BGRSLV04-14
Sample Name
Sample Name	KDM5A-BGRSLV04-13	KDM5A-BGRSLV04-14
RBP	KDM5A	KDM5A
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	11442	11443

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-13	BGRSLV04-14
Sample #	7	8
Sample Name	KDM5A-BGRSLV04-13	KDM5A-BGRSLV04-14
Sample_Name_Alias
Index Well Position	G01	H01
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	288	290
Peak_Molarity	62.70	31.90
libSampleQC_DNA_Well	DNA_Library_set59/set1/G7.png	DNA_Library_set59/set1/H7.png
RIN	9.8	8.9
libSample_RNA_Well	RNA_Library_set59/set1/G2.png	RNA_Library_set59/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-13	BGRSLV04-14
RBP	KDM5A	KDM5A
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	3556	3557

Sequencing Information

	BGRSLV04-13	BGRSLV04-14
Sample_ID	BGRSLV04-13	BGRSLV04-14
Sample Name	KDM5A-BGRSLV04-13	KDM5A-BGRSLV04-14
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	52,094,885	46,365,713
total_aligned_reads	43,911,788	33,115,626
unique_aligned_reads	40,696,078	30,493,055
percent_uniqueAligned	0.78119	0.65766
correlation_replicates	0.985134	0.985134
spikein_reads	207,646	170,888
percent_spikeins	0.00399	0.00369
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2427	2428

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
KDM5A-BGRSLV04-13_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2427	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	8054
KDM5A-BGRSLV04-13_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2427	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	8092
KDM5A-BGRSLV04-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2427					GRCh38	V40	KDM5A-BGRSLV04-13_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,KDM5A-BGRSLV04-13_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11023
KDM5A-BGRSLV04-13_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	2427					GRCh38	V40	KDM5A-BGRSLV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	11061
KDM5A-BGRSLV04-13_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	2427					GRCh38	V40	KDM5A-BGRSLV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	11099
KDM5A-BGRSLV04-13_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	2427					GRCh38	V40	KDM5A-BGRSLV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	11137
KDM5A-BGRSLV04-13_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	2427					GRCh38	V40	KDM5A-BGRSLV04-13/Aligned.sortedByCoord.out.bam		ENCORE2	11175
KDM5A-BGRSLV04-13_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2427					GRCh38	V40	KDM5A-BGRSLV04-13_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,KDM5A-BGRSLV04-13_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11213
KDM5A-BGRSLV04-14_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2428	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	8055
KDM5A-BGRSLV04-14_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2428	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	8093
KDM5A-BGRSLV04-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2428					GRCh38	V40	KDM5A-BGRSLV04-14_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,KDM5A-BGRSLV04-14_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11024
KDM5A-BGRSLV04-14_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	2428					GRCh38	V40	KDM5A-BGRSLV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	11062
KDM5A-BGRSLV04-14_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	2428					GRCh38	V40	KDM5A-BGRSLV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	11100
KDM5A-BGRSLV04-14_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	2428					GRCh38	V40	KDM5A-BGRSLV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	11138
KDM5A-BGRSLV04-14_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	2428					GRCh38	V40	KDM5A-BGRSLV04-14/Aligned.sortedByCoord.out.bam		ENCORE2	11176
KDM5A-BGRSLV04-14_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2428					GRCh38	V40	KDM5A-BGRSLV04-14_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,KDM5A-BGRSLV04-14_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11214