CHCHD3 RNA-Seq in K562

General Information


RBP	CHCHD3
Cell_Line	K562
Method	CRISPR
Exp_Name	CHCHD3-BGKcLV28-K562
ENCODE_series_ID	ENCSR221MPE
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR307GHU
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CHCHD3-BGKcLV28-17
Rep2	CHCHD3-BGKcLV28-18
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	52.7
Rep2_qPCR	60.3
Rep1_WB	53.8
Rep2_WB	51.6
Antibody Cat#	A305-497A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB646GEA
Status	Released
Project	ENCODE4
ID	825

Experiment Information (Status: Released)

	BGKcLV28-17	BGKcLV28-18
idx	951	952
TRCN#_or_BGC#	BGC#0000694	BGC#0000694
shRNA_or_gRNA_sequence	CAGGAACCGGAATCATGGGT	CAGGAACCGGAATCATGGGT
PAM	GGG	GGG
Name	CHCHD3_81	CHCHD3_81
Sample_ID	BGKcLV28-17	BGKcLV28-18
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CHCHD3	CHCHD3
qPCR_result	52.7	60.3
Ave_qPCR	56.5
RT-qPCR_primer-F	aaagctgctgaagaggtgga
RT-qPCR_primer-R	ggtctggtgggtgttctcac
protein_conc	1835	1733
WB_result	53.8	51.6
Ave_WB	52.7
WB_DONE_date	8/26/21	need discusstion
MW	26kd
IP
antibody_Cat#	A305-497A	LOT #1
Antibody DCC ID	ENCAB646GEA	1/19/22
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/23/21	09/23/21
repeat_library
Note
ID	5085	5086

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

	BGKcLV28-17	BGKcLV28-18
Sample_ID	BGKcLV28-17	BGKcLV28-18
Sample Name
Sample Name	CHCHD3-BGKcLV28-17	CHCHD3-BGKcLV28-18
RBP	CHCHD3	CHCHD3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9909	9910

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-17	BGKcLV28-18
Sample #	17	18
Sample Name	CHCHD3-BGKcLV28-17	CHCHD3-BGKcLV28-18
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-21	2021-09-21
Lib_ID	Lib-210921	Lib-210921
Tecan_Location
Tecan
Tecan_date
Size_bp	325	333
Peak_Molarity	99.20	108.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/A3.png	DNA_Library_set48-49/set3/B3.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set48-49/set2/A3.png	RNA_Library_set48-49/set2/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-17	BGKcLV28-18
RBP	CHCHD3	CHCHD3
Batch_ID	BGKcLV28	BGKcLV28
WB_result	53.800	51.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2078	2079

Sequencing Information

	BGKcLV28-17	BGKcLV28-18
Sample_ID	BGKcLV28-17	BGKcLV28-18
Sample Name	CHCHD3-BGKcLV28-17	CHCHD3-BGKcLV28-18
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	80,059,256	95,925,434
total_aligned_reads	74,575,050	83,309,370
unique_aligned_reads	68,720,502	76,513,202
percent_uniqueAligned	0.85837	0.79763
correlation_replicates	0.983815	0.983815
spikein_reads	27,330	20,692
percent_spikeins	0.00034	0.00022
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1829	1830

Data Submission Information

	BGKcLV28-17	BGKcLV28-17	BGKcLV28-17	BGKcLV28-17	BGKcLV28-17	BGKcLV28-17	BGKcLV28-18	BGKcLV28-18	BGKcLV28-18	BGKcLV28-18
ENCODE_alias	brenton-graveley:CHCHD3-BGKcLV28	brenton-graveley:CHCHD3-BGKcLV28-17	brenton-graveley:L-CHCHD3-BGKcLV28-17	brenton-graveley:CHCHD3-BGKcLV28-17_S99_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHCHD3-BGKcLV28-17_S99_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHCHD3-BGKcLV28-K562	brenton-graveley:CHCHD3-BGKcLV28-18	brenton-graveley:L-CHCHD3-BGKcLV28-18	brenton-graveley:CHCHD3-BGKcLV28-18_S100_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CHCHD3-BGKcLV28-18_S100_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR307GHU	ENCBS129MBJ	ENCLB736RXW	ENCFF062SVC	ENCFF146CRR	ENCSR221MPE	ENCBS249NVQ	ENCLB260VRJ	ENCFF477NYJ	ENCFF647RRB
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	BGKcLV28-17	BGKcLV28-17	BGKcLV28-17	BGKcLV28-17	BGKcLV28-17	BGKcLV28-17	BGKcLV28-18	BGKcLV28-18	BGKcLV28-18	BGKcLV28-18
Sample Name	CHCHD3-BGKcLV28-17	CHCHD3-BGKcLV28-17	CHCHD3-BGKcLV28-17	CHCHD3-BGKcLV28-17	CHCHD3-BGKcLV28-17	CHCHD3-BGKcLV28-17	CHCHD3-BGKcLV28-18	CHCHD3-BGKcLV28-18	CHCHD3-BGKcLV28-18	CHCHD3-BGKcLV28-18
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-03-02	2022-01-29	2022-01-29	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV49_biosample_protocol	LV49_library_protocol				LV49_biosample_protocol	LV49_library_protocol
protocol_URL		CHCHD3-BGKcLV28-17.pdf	L-CHCHD3-BGKcLV28-17.pdf				CHCHD3-BGKcLV28-18.pdf	L-CHCHD3-BGKcLV28-18.pdf
ID	3479	3592	3726	3860	3994	7134	3593	3727	3861	3995

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-BGKcLV28-17_S99_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1829	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3946
CHCHD3-BGKcLV28-17_S99_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1829	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4004
CHCHD3-BGKcLV28-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1829					GRCh38	V40	CHCHD3-BGKcLV28-17_S99_L004_R1_001.filtered.trimmed.paired.fastq.gz,CHCHD3-BGKcLV28-17_S99_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19228
CHCHD3-BGKcLV28-17_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1829					GRCh38	V40	CHCHD3-BGKcLV28-17/Aligned.sortedByCoord.out.bam		ENCORE2	19286
CHCHD3-BGKcLV28-17_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1829					GRCh38	V40	CHCHD3-BGKcLV28-17/Aligned.sortedByCoord.out.bam		ENCORE2	19344
CHCHD3-BGKcLV28-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1829					GRCh38	V40	CHCHD3-BGKcLV28-17/Aligned.sortedByCoord.out.bam		ENCORE2	19402
CHCHD3-BGKcLV28-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1829					GRCh38	V40	CHCHD3-BGKcLV28-17/Aligned.sortedByCoord.out.bam		ENCORE2	19460
CHCHD3-BGKcLV28-17_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1829					GRCh38	V40	CHCHD3-BGKcLV28-17_S99_L004_R1_001.filtered.trimmed.paired.fastq.gz,CHCHD3-BGKcLV28-17_S99_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19518
CHCHD3-BGKcLV28-18_S100_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1830	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3947
CHCHD3-BGKcLV28-18_S100_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1830	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4005
CHCHD3-BGKcLV28-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1830					GRCh38	V40	CHCHD3-BGKcLV28-18_S100_L004_R1_001.filtered.trimmed.paired.fastq.gz,CHCHD3-BGKcLV28-18_S100_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19229
CHCHD3-BGKcLV28-18_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1830					GRCh38	V40	CHCHD3-BGKcLV28-18/Aligned.sortedByCoord.out.bam		ENCORE2	19287
CHCHD3-BGKcLV28-18_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1830					GRCh38	V40	CHCHD3-BGKcLV28-18/Aligned.sortedByCoord.out.bam		ENCORE2	19345
CHCHD3-BGKcLV28-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1830					GRCh38	V40	CHCHD3-BGKcLV28-18/Aligned.sortedByCoord.out.bam		ENCORE2	19403
CHCHD3-BGKcLV28-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1830					GRCh38	V40	CHCHD3-BGKcLV28-18/Aligned.sortedByCoord.out.bam		ENCORE2	19461
CHCHD3-BGKcLV28-18_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1830					GRCh38	V40	CHCHD3-BGKcLV28-18_S100_L004_R1_001.filtered.trimmed.paired.fastq.gz,CHCHD3-BGKcLV28-18_S100_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19519