CHMP7 RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV47-7	BGHcLV47-8
idx	1611	1612
TRCN#_or_BGC#	BGC#0001225	BGC#0001225
shRNA_or_gRNA_sequence	AGGAGGCCTTTCAGCGCAAG	AGGAGGCCTTTCAGCGCAAG
PAM	GGG	GGG
Name	CHMP7_89B	CHMP7_89B
Sample_ID	BGHcLV47-7	BGHcLV47-8
transduction_Date	1/28/25	1/28/25
days	D6	D6
RBP_name	CHMP7	CHMP7
qPCR_result	67.0	60.0
Ave_qPCR	63.5
RT-qPCR_primer-F	gtctctcaaggccaagcaac
RT-qPCR_primer-R	cagcctggtaggcgttaaaa
protein_conc	3817	3800
WB_result	91.2	88.3
Ave_WB
WB_DONE_date	2/5/25
MW	51kd
IP	Rabbit / I
antibody_Cat#	A305-734A-M	lot # 1
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	9800	9801

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CHMP7	Product_ID: A305-734A-M Lot_ID: 1 Source: Bethyl Labs Target Name: CHMP7-human

Experiment Status

	BGHcLV47-7	BGHcLV47-8
Sample_ID	BGHcLV47-7	BGHcLV47-8
Sample Name
Sample Name	CHMP7-BGHcLV47-7	CHMP7-BGHcLV47-8
RBP	CHMP7	CHMP7
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-05-14	2025-05-14
Project	ENCORE2	ENCORE2
Note
ID	14152	14153

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-7	BGHcLV47-8
Sample #	5	6
Sample Name	CHMP7-BGHcLV47-7	CHMP7-BGHcLV47-8
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-04-23	2025-04-23
Lib_ID	Lib-250423	Lib-250423
Tecan_Location
Tecan
Tecan_date
Size_bp	268	257
Peak_Molarity	53.50	69.80
libSampleQC_DNA_Well	DNA_Library_set78/set1/E6.png	DNA_Library_set78/set1/F6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set78/set1/E1.png	RNA_Library_set78/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-7	BGHcLV47-8
RBP	CHMP7	CHMP7
Batch_ID	BGHcLV47	BGHcLV47
WB_result	91.200	88.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4716	4717

Sequencing Information

	BGHcLV47-7	BGHcLV47-8
Sample_ID	BGHcLV47-7	BGHcLV47-8
Sample Name	CHMP7-BGHcLV47-7	CHMP7-BGHcLV47-8
Pool ID	Pool-250422	Pool-250422
LocalServer_folder	set78	set78
total_reads	19,118,932	13,375,740
total_aligned_reads	16,355,524	11,005,947
unique_aligned_reads	15,383,780	10,381,295
percent_uniqueAligned	0.80464	0.77613
correlation_replicates	0.993473	0.993473
spikein_reads	20,328	10,370
percent_spikeins	0.00106	0.00078
original_ReadLength	101	101
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3419	3420

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
CHMP7-BGHcLV47-7_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3419	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32550
CHMP7-BGHcLV47-7_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3419	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32584
CHMP7-BGHcLV47-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3419					GRCh38	V40	CHMP7-BGHcLV47-7_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz,CHMP7-BGHcLV47-7_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32618
CHMP7-BGHcLV47-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3419					GRCh38	V40	CHMP7-BGHcLV47-7_Aligned.sortedByCoord.out.bam		ENCORE2	32652
CHMP7-BGHcLV47-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3419					GRCh38	V40	CHMP7-BGHcLV47-7_Aligned.sortedByCoord.out.bam		ENCORE2	32686
CHMP7-BGHcLV47-7_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3419					GRCh38	V40	CHMP7-BGHcLV47-7_Aligned.sortedByCoord.out.bam		ENCORE2	32720
CHMP7-BGHcLV47-7_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3419					GRCh38	V40	CHMP7-BGHcLV47-7_Aligned.sortedByCoord.out.bam		ENCORE2	32754
CHMP7-BGHcLV47-7_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3419					GRCh38	V40	CHMP7-BGHcLV47-7_S46_L002_R1_001.filtered.trimmed.paired.fastq.gz,CHMP7-BGHcLV47-7_S46_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32788
CHMP7-BGHcLV47-8_S47_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3420	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32551
CHMP7-BGHcLV47-8_S47_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3420	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32585
CHMP7-BGHcLV47-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3420					GRCh38	V40	CHMP7-BGHcLV47-8_S47_L002_R1_001.filtered.trimmed.paired.fastq.gz,CHMP7-BGHcLV47-8_S47_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32619
CHMP7-BGHcLV47-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3420					GRCh38	V40	CHMP7-BGHcLV47-8_Aligned.sortedByCoord.out.bam		ENCORE2	32653
CHMP7-BGHcLV47-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3420					GRCh38	V40	CHMP7-BGHcLV47-8_Aligned.sortedByCoord.out.bam		ENCORE2	32687
CHMP7-BGHcLV47-8_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3420					GRCh38	V40	CHMP7-BGHcLV47-8_Aligned.sortedByCoord.out.bam		ENCORE2	32721
CHMP7-BGHcLV47-8_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3420					GRCh38	V40	CHMP7-BGHcLV47-8_Aligned.sortedByCoord.out.bam		ENCORE2	32755
CHMP7-BGHcLV47-8_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3420					GRCh38	V40	CHMP7-BGHcLV47-8_S47_L002_R1_001.filtered.trimmed.paired.fastq.gz,CHMP7-BGHcLV47-8_S47_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32789