CMTR1 RNA-Seq in HepG2

General Information


RBP	CMTR1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CMTR1-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR281QCJ
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR244OOV
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CMTR1-BGHcLV29-25
Rep2	CMTR1-BGHcLV29-26
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	73.4
Rep2_qPCR	77.8
Rep1_WB	76.9
Rep2_WB	75.9
Antibody Cat#	A300-304A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB409TEB
Status	Submitted
Project	ENCODE4
ID	853

Experiment Information (Status: Released)

	BGHcLV29-25	BGHcLV29-25	BGHcLV29-26	BGHcLV29-26
idx	856	858	857	859
TRCN#_or_BGC#	BGC#0000701	BGC#0000701	BGC#0000701	BGC#0000701
shRNA_or_gRNA_sequence	GGGAGGTTCATCATCGGACG	GGGAGGTTCATCATCGGACG	GGGAGGTTCATCATCGGACG	GGGAGGTTCATCATCGGACG
PAM	TGG	TGG	TGG	TGG
Name	CMTR1_94	CMTR1_94	CMTR1_94	CMTR1_94
Sample_ID	BGHcLV29-25	BGHcLV29-25	BGHcLV29-26	BGHcLV29-26
transduction_Date	7/20	7/20	7/20	7/20
days	D6	D6	D6	D6
RBP_name	CMTR1	CMTR1	CMTR1	CMTR1
qPCR_result	73.4	73.4	77.8	77.8
Ave_qPCR		75.6
RT-qPCR_primer-F		gctttgaccaggagctgaac
RT-qPCR_primer-R		accatccaatcgctcatttc
protein_conc	3460	3460	4764	4764
WB_result	76.9	86.2247674	75.9	94.4
Ave_WB	76.4	90.3
WB_DONE_date	10/26/21	10/27/21	JESS
MW	95kd	95kd
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A300-304A	A300-303A	LOT #1	LOT #2
Antibody DCC ID	ENCAB409TEB
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action		Ready		Ready
Library_start_date		11/5/21		11/5/21
repeat_library
Note
ID	7033	7035	7034	7036

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV29-25	BGHcLV29-25	BGHcLV29-26	BGHcLV29-26
Sample_ID	BGHcLV29-25	BGHcLV29-25	BGHcLV29-26	BGHcLV29-26
Sample Name
Sample Name	CMTR1-BGHcLV29-25		CMTR1-BGHcLV29-26
RBP	CMTR1	CMTR1	CMTR1	CMTR1
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2022-02-11	2021-10-28	2022-02-11	2021-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	9991	10025	9992	10026

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-25	BGHcLV29-26
Sample #	19	20
Sample Name	CMTR1-BGHcLV29-25	CMTR1-BGHcLV29-26
Sample_Name_Alias
Index Well Position	C03	D03
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	291	291
Peak_Molarity	38.10	37.70
libSampleQC_DNA_Well	DNA_Library_set50/set1/C3.png	DNA_Library_set50/set1/D3.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set50/set1/C9.png	RNA_Library_set50/set1/D9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-25	BGHcLV29-26
RBP	CMTR1	CMTR1
Batch_ID	BGHcLV29	BGHcLV29
WB_result	86.225	94.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3106	3107

Sequencing Information

	BGHcLV29-25	BGHcLV29-26
Sample_ID	BGHcLV29-25	BGHcLV29-26
Sample Name	CMTR1-BGHcLV29-25	CMTR1-BGHcLV29-26
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	79,379,490	73,255,466
total_aligned_reads	70,980,974	67,306,554
unique_aligned_reads	66,980,274	63,488,728
percent_uniqueAligned	0.84380	0.86668
correlation_replicates	0.991284	0.991284
spikein_reads	17,984	9,456
percent_spikeins	0.00023	0.00013
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1887	1888

Data Submission Information

	BGHcLV29-25	BGHcLV29-25	BGHcLV29-25	BGHcLV29-25	BGHcLV29-25	BGHcLV29-25	BGHcLV29-26	BGHcLV29-26	BGHcLV29-26	BGHcLV29-26
ENCODE_alias	brenton-graveley:CMTR1-BGHcLV29	brenton-graveley:CMTR1-BGHcLV29-25	brenton-graveley:L-CMTR1-BGHcLV29-25	brenton-graveley:CMTR1-BGHcLV29-25_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CMTR1-BGHcLV29-25_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CMTR1-BGHcLV29-HepG2	brenton-graveley:CMTR1-BGHcLV29-26	brenton-graveley:L-CMTR1-BGHcLV29-26	brenton-graveley:CMTR1-BGHcLV29-26_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CMTR1-BGHcLV29-26_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR244OOV	ENCBS662RQC	ENCLB127EOR	ENCFF445HWK	ENCFF103RSH	ENCSR281QCJ	ENCBS154QKL	ENCLB604IRA	ENCFF493WFV	ENCFF528SGS
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	BGHcLV29-25	BGHcLV29-25	BGHcLV29-25	BGHcLV29-25	BGHcLV29-25	BGHcLV29-25	BGHcLV29-26	BGHcLV29-26	BGHcLV29-26	BGHcLV29-26
Sample Name	CMTR1-BGHcLV29-25	CMTR1-BGHcLV29-25	CMTR1-BGHcLV29-25	CMTR1-BGHcLV29-25	CMTR1-BGHcLV29-25	CMTR1-BGHcLV29-25	CMTR1-BGHcLV29-26	CMTR1-BGHcLV29-26	CMTR1-BGHcLV29-26	CMTR1-BGHcLV29-26
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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_library_protocol					LV50H_library_protocol
protocol_URL			L-CMTR1-BGHcLV29-25.pdf					L-CMTR1-BGHcLV29-26.pdf
ID	5851	5895	5967	6039	6111	6174	5896	5968	6040	6112

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
CMTR1-BGHcLV29-25_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1887	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	5775
CMTR1-BGHcLV29-25_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1887	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	5817
CMTR1-BGHcLV29-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1887					GRCh38	V40	CMTR1-BGHcLV29-25_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,CMTR1-BGHcLV29-25_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18942
CMTR1-BGHcLV29-25_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	1887					GRCh38	V40	CMTR1-BGHcLV29-25/Aligned.sortedByCoord.out.bam		ENCORE2	19000
CMTR1-BGHcLV29-25_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	1887					GRCh38	V40	CMTR1-BGHcLV29-25/Aligned.sortedByCoord.out.bam		ENCORE2	19046
CMTR1-BGHcLV29-25_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	1887					GRCh38	V40	CMTR1-BGHcLV29-25/Aligned.sortedByCoord.out.bam		ENCORE2	19092
CMTR1-BGHcLV29-25_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	1887					GRCh38	V40	CMTR1-BGHcLV29-25/Aligned.sortedByCoord.out.bam		ENCORE2	19138
CMTR1-BGHcLV29-25_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1887					GRCh38	V40	CMTR1-BGHcLV29-25_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,CMTR1-BGHcLV29-25_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19184
CMTR1-BGHcLV29-26_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1888	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	5776
CMTR1-BGHcLV29-26_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1888	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	5818
CMTR1-BGHcLV29-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1888					GRCh38	V40	CMTR1-BGHcLV29-26_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,CMTR1-BGHcLV29-26_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18943
CMTR1-BGHcLV29-26_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	1888					GRCh38	V40	CMTR1-BGHcLV29-26/Aligned.sortedByCoord.out.bam		ENCORE2	19001
CMTR1-BGHcLV29-26_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	1888					GRCh38	V40	CMTR1-BGHcLV29-26/Aligned.sortedByCoord.out.bam		ENCORE2	19047
CMTR1-BGHcLV29-26_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	1888					GRCh38	V40	CMTR1-BGHcLV29-26/Aligned.sortedByCoord.out.bam		ENCORE2	19093
CMTR1-BGHcLV29-26_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	1888					GRCh38	V40	CMTR1-BGHcLV29-26/Aligned.sortedByCoord.out.bam		ENCORE2	19139
CMTR1-BGHcLV29-26_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1888					GRCh38	V40	CMTR1-BGHcLV29-26_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,CMTR1-BGHcLV29-26_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19185