CHCHD3 RNA-Seq in HepG2

General Information


RBP	CHCHD3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CHCHD3-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR840OSW
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR206ICZ
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CHCHD3-BGHcLV29-17
Rep2	CHCHD3-BGHcLV29-18
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	63
Rep2_qPCR	53.4
Rep1_WB	57.1
Rep2_WB	59.8
Antibody Cat#	A305-497A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB646GEA
Status	Submitted
Project	ENCODE4
ID	850

Experiment Information (Status: Released)

	BGHcLV29-17	BGHcLV29-18
idx	848	849
TRCN#_or_BGC#	BGC#0000694	BGC#0000694
shRNA_or_gRNA_sequence	CAGGAACCGGAATCATGGGT	CAGGAACCGGAATCATGGGT
PAM	GGG	GGG
Name	CHCHD3_81	CHCHD3_81
Sample_ID	BGHcLV29-17	BGHcLV29-18
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	CHCHD3	CHCHD3
qPCR_result	63	53.4
Ave_qPCR	58.2
RT-qPCR_primer-F	aaagctgctgaagaggtgga
RT-qPCR_primer-R	ggtctggtgggtgttctcac
protein_conc	0	4232
WB_result	57.1	59.8
Ave_WB	58.4
WB_DONE_date	10/26/21	JESS
MW	26kd
IP	Rabbit / I
antibody_Cat#	A305-497A	LOT #1
Antibody DCC ID	ENCAB646GEA
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/5/21	11/5/21
repeat_library
Note
ID	9073	9074

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CHCHD3	Product_ID: A305-497A Lot_ID: 1 Source: Bethyl Labs Target Name: CHCHD3-human

Experiment Status

	BGHcLV29-17	BGHcLV29-18
Sample_ID	BGHcLV29-17	BGHcLV29-18
Sample Name
Sample Name	CHCHD3-BGHcLV29-17	CHCHD3-BGHcLV29-18
RBP	CHCHD3	CHCHD3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9985	9986

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-17	BGHcLV29-18
Sample #	13	14
Sample Name	CHCHD3-BGHcLV29-17	CHCHD3-BGHcLV29-18
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	293	295
Peak_Molarity	47.70	42.00
libSampleQC_DNA_Well	DNA_Library_set50/set1/E2.png	DNA_Library_set50/set1/F2.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set50/set1/E8.png	RNA_Library_set50/set1/F8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-17	BGHcLV29-18
RBP	CHCHD3	CHCHD3
Batch_ID	BGHcLV29	BGHcLV29
WB_result	57.100	59.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3100	3101

Sequencing Information

	BGHcLV29-17	BGHcLV29-18
Sample_ID	BGHcLV29-17	BGHcLV29-18
Sample Name	CHCHD3-BGHcLV29-17	CHCHD3-BGHcLV29-18
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	79,334,290	67,365,494
total_aligned_reads	75,007,758	63,926,802
unique_aligned_reads	70,804,094	60,339,852
percent_uniqueAligned	0.89248	0.89571
correlation_replicates	0.998977	0.998977
spikein_reads	23,050	18,292
percent_spikeins	0.00029	0.00027
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1881	1882

Data Submission Information

	BGHcLV29-17	BGHcLV29-17	BGHcLV29-17	BGHcLV29-17	BGHcLV29-17	BGHcLV29-17	BGHcLV29-18	BGHcLV29-18	BGHcLV29-18	BGHcLV29-18
ENCODE_alias	brenton-graveley:CHCHD3-BGHcLV29	brenton-graveley:CHCHD3-BGHcLV29-17	brenton-graveley:L-CHCHD3-BGHcLV29-17	brenton-graveley:CHCHD3-BGHcLV29-17_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHCHD3-BGHcLV29-17_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHCHD3-BGHcLV29-HepG2	brenton-graveley:CHCHD3-BGHcLV29-18	brenton-graveley:L-CHCHD3-BGHcLV29-18	brenton-graveley:CHCHD3-BGHcLV29-18_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHCHD3-BGHcLV29-18_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR206ICZ	ENCBS950SXM	ENCLB773IQI	ENCFF819MPX	ENCFF840VGM	ENCSR840OSW	ENCBS907ALU	ENCLB971MRZ	ENCFF461TFE	ENCFF818RZP
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV29-17	BGHcLV29-17	BGHcLV29-17	BGHcLV29-17	BGHcLV29-17	BGHcLV29-17	BGHcLV29-18	BGHcLV29-18	BGHcLV29-18	BGHcLV29-18
Sample Name	CHCHD3-BGHcLV29-17	CHCHD3-BGHcLV29-17	CHCHD3-BGHcLV29-17	CHCHD3-BGHcLV29-17	CHCHD3-BGHcLV29-17	CHCHD3-BGHcLV29-17	CHCHD3-BGHcLV29-18	CHCHD3-BGHcLV29-18	CHCHD3-BGHcLV29-18	CHCHD3-BGHcLV29-18
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50H_biosample_protocol	LV50H_library_protocol				LV50H_biosample_protocol	LV50H_library_protocol
protocol_URL		CHCHD3-BGHcLV29-17.pdf	L-CHCHD3-BGHcLV29-17.pdf				CHCHD3-BGHcLV29-18.pdf	L-CHCHD3-BGHcLV29-18.pdf
ID	5848	5889	5961	6033	6105	6171	5890	5962	6034	6106

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
CHCHD3-BGHcLV29-17_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1881	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5769
CHCHD3-BGHcLV29-17_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1881	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5811
CHCHD3-BGHcLV29-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1881					GRCh38	V40	CHCHD3-BGHcLV29-17_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHCHD3-BGHcLV29-17_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18936
CHCHD3-BGHcLV29-17_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1881					GRCh38	V40	CHCHD3-BGHcLV29-17/Aligned.sortedByCoord.out.bam		ENCORE2	18994
CHCHD3-BGHcLV29-17_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1881					GRCh38	V40	CHCHD3-BGHcLV29-17/Aligned.sortedByCoord.out.bam		ENCORE2	19040
CHCHD3-BGHcLV29-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1881					GRCh38	V40	CHCHD3-BGHcLV29-17/Aligned.sortedByCoord.out.bam		ENCORE2	19086
CHCHD3-BGHcLV29-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1881					GRCh38	V40	CHCHD3-BGHcLV29-17/Aligned.sortedByCoord.out.bam		ENCORE2	19132
CHCHD3-BGHcLV29-17_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1881					GRCh38	V40	CHCHD3-BGHcLV29-17_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHCHD3-BGHcLV29-17_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19178
CHCHD3-BGHcLV29-18_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1882	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5770
CHCHD3-BGHcLV29-18_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1882	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5812
CHCHD3-BGHcLV29-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1882					GRCh38	V40	CHCHD3-BGHcLV29-18_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHCHD3-BGHcLV29-18_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18937
CHCHD3-BGHcLV29-18_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1882					GRCh38	V40	CHCHD3-BGHcLV29-18/Aligned.sortedByCoord.out.bam		ENCORE2	18995
CHCHD3-BGHcLV29-18_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1882					GRCh38	V40	CHCHD3-BGHcLV29-18/Aligned.sortedByCoord.out.bam		ENCORE2	19041
CHCHD3-BGHcLV29-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1882					GRCh38	V40	CHCHD3-BGHcLV29-18/Aligned.sortedByCoord.out.bam		ENCORE2	19087
CHCHD3-BGHcLV29-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1882					GRCh38	V40	CHCHD3-BGHcLV29-18/Aligned.sortedByCoord.out.bam		ENCORE2	19133
CHCHD3-BGHcLV29-18_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1882					GRCh38	V40	CHCHD3-BGHcLV29-18_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,CHCHD3-BGHcLV29-18_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19179