CHMP7 RNA-Seq in K562

General Information


RBP	CHMP7
Cell_Line	K562
Method	CRISPR
Exp_Name	CHMP7-BGKcLV46-K562
ENCODE_series_ID
Batch_ID	BGKcLV46
Pool ID	Pool-250312
Local_Set_Name	set77
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CHMP7-BGKcLV46-5
Rep2	CHMP7-BGKcLV46-6
CN1	NT-BGKcLV46-1
CN2	NT-BGKcLV46-2
Rep1_qPCR	62.3
Rep2_qPCR	59.4
Rep1_WB	74.1
Rep2_WB	67.1
Antibody Cat#	A305-734A-M
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1635

Experiment Information (Status: Submitting)

	BGKcLV46-5	BGKcLV46-6
idx	0	0
TRCN#_or_BGC#	BGC#0001225	BGC#0001225
shRNA_or_gRNA_sequence	AGGAGGCCTTTCAGCGCAAG	AGGAGGCCTTTCAGCGCAAG
PAM	GGG	GGG
Name	CHMP7_89B	CHMP7_89B
Sample_ID	BGKcLV46-5	BGKcLV46-6
transduction_Date	12/20/24	12/20/24
days	D6	D6
RBP_name	CHMP7	CHMP7
qPCR_result	62.3	59.4
Ave_qPCR	60.9
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3462	3424
WB_result	74.1	67.1
Ave_WB
WB_DONE_date	12/31/24,1/23/25
MW	51kd
IP
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	5991	5992

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

	BGKcLV46-5	BGKcLV46-6
Sample_ID	BGKcLV46-5	BGKcLV46-6
Sample Name
Sample Name	CHMP7-BGKcLV46-5	CHMP7-BGKcLV46-6
RBP	CHMP7	CHMP7
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	14024	14025

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV46-5	BGKcLV46-6
Sample #	3	4
Sample Name	CHMP7-BGKcLV46-5	CHMP7-BGKcLV46-6
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-02-20	2025-02-20
Lib_ID	Lib-250220	Lib-250220
Tecan_Location
Tecan
Tecan_date
Size_bp	297	299
Peak_Molarity	85.50	95.60
libSampleQC_DNA_Well	DNA_Library_set77/set1/C7.png	DNA_Library_set77/set1/D7.png
RIN	9.7	10.0
libSample_RNA_Well	RNA_Library_set77/set1/C1.png	RNA_Library_set77/set1/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-02-28	2025-02-28
Sample_ID	BGKcLV46-5	BGKcLV46-6
RBP	CHMP7	CHMP7
Batch_ID	BGKcLV46	BGKcLV46
WB_result	74.100	67.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4662	4663

Sequencing Information

	BGKcLV46-5	BGKcLV46-6
Sample_ID	BGKcLV46-5	BGKcLV46-6
Sample Name	CHMP7-BGKcLV46-5	CHMP7-BGKcLV46-6
Pool ID	Pool-250312	Pool-250312
LocalServer_folder	set77	set77
total_reads	57,756,002	51,342,921
total_aligned_reads	52,674,800	47,348,296
unique_aligned_reads	48,421,282	43,600,697
percent_uniqueAligned	0.83838	0.84921
correlation_replicates	0.989171	0.989171
spikein_reads	264,330	122,920
percent_spikeins	0.00458	0.00239
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3367	3368

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-BGKcLV46-5_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3367	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32148
CHMP7-BGKcLV46-5_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3367	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32198
CHMP7-BGKcLV46-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3367					GRCh38	V40	CHMP7-BGKcLV46-5_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHMP7-BGKcLV46-5_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32248
CHMP7-BGKcLV46-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3367					GRCh38	V40	CHMP7-BGKcLV46-5_Aligned.sortedByCoord.out.bam		ENCORE2	32298
CHMP7-BGKcLV46-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3367					GRCh38	V40	CHMP7-BGKcLV46-5_Aligned.sortedByCoord.out.bam		ENCORE2	32348
CHMP7-BGKcLV46-5_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3367					GRCh38	V40	CHMP7-BGKcLV46-5_Aligned.sortedByCoord.out.bam		ENCORE2	32398
CHMP7-BGKcLV46-5_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3367					GRCh38	V40	CHMP7-BGKcLV46-5_Aligned.sortedByCoord.out.bam		ENCORE2	32448
CHMP7-BGKcLV46-5_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3367					GRCh38	V40	CHMP7-BGKcLV46-5_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHMP7-BGKcLV46-5_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32498
CHMP7-BGKcLV46-6_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3368	NovaSeq6000	100	paired-ended	1				NT-BGKcLV46-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32149
CHMP7-BGKcLV46-6_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set77/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3368	NovaSeq6000	100	paired-ended	2				NT-BGKcLV46-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV46-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32199
CHMP7-BGKcLV46-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3368					GRCh38	V40	CHMP7-BGKcLV46-6_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHMP7-BGKcLV46-6_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32249
CHMP7-BGKcLV46-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3368					GRCh38	V40	CHMP7-BGKcLV46-6_Aligned.sortedByCoord.out.bam		ENCORE2	32299
CHMP7-BGKcLV46-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3368					GRCh38	V40	CHMP7-BGKcLV46-6_Aligned.sortedByCoord.out.bam		ENCORE2	32349
CHMP7-BGKcLV46-6_Signal.Unique.strand-.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3368					GRCh38	V40	CHMP7-BGKcLV46-6_Aligned.sortedByCoord.out.bam		ENCORE2	32399
CHMP7-BGKcLV46-6_Signal.Unique.strand+.bw	ENCODE_DATA/set77/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3368					GRCh38	V40	CHMP7-BGKcLV46-6_Aligned.sortedByCoord.out.bam		ENCORE2	32449
CHMP7-BGKcLV46-6_quant.sf	ENCODE_DATA/set77/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3368					GRCh38	V40	CHMP7-BGKcLV46-6_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHMP7-BGKcLV46-6_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32499