CMTR1 RNA-Seq in K562

General Information


RBP	CMTR1
Cell_Line	K562
Method	CRISPR
Exp_Name	CMTR1-BGKcLV28-K562
ENCODE_series_ID	ENCSR169WSA
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR697NDQ
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CMTR1-BGKcLV28-25
Rep2	CMTR1-BGKcLV28-26
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	70.2
Rep2_WB	71.1
Antibody Cat#	A300-303A
Antibody Lot#	LOT #2
Antibody DCC ID	ENCAB701WNM
Status	Released
Project	ENCODE4
ID	829

Experiment Information (Status: Released)

	BGKcLV28-25	BGKcLV28-25	BGKcLV28-26	BGKcLV28-26
idx	959	961	960	962
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	BGKcLV28-25	BGKcLV28-25	BGKcLV28-26	BGKcLV28-26
transduction_Date	7/12/21	7/12/21	7/12/21	7/12/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	CMTR1	CMTR1	CMTR1	CMTR1
qPCR_result	54.2	54.2	60.1	60.1
Ave_qPCR	57.2	57.2
RT-qPCR_primer-F	gctttgaccaggagctgaac	gctttgaccaggagctgaac
RT-qPCR_primer-R	accatccaatcgctcatttc	accatccaatcgctcatttc
protein_conc	1829	1829	1995	1995
WB_result	70.2	55.6	71.1	65.885289
Ave_WB	70.7	60.7
WB_DONE_date	6/29/21	8/25/21	JESS	JESS
MW	95kd	95kd
IP
antibody_Cat#	A300-303A	A300-304A	LOT #2	LOT #1
Antibody DCC ID	ENCAB958TIL	ENCAB409TEB	1/19/22	1/19/22
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/23/21		09/23/21
repeat_library
Note
ID	5093	5095	5094	5096

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CMTR1	Product_ID: A300-303A Lot_ID: 2 Source: Bethyl Labs Target Name: CMTR1-human
CMTR1	Product_ID: A300-304A Lot_ID: 1 Source: Bethyl Labs Target Name: CMTR1-human

Experiment Status

	BGKcLV28-25	BGKcLV28-25	BGKcLV28-26	BGKcLV28-26
Sample_ID	BGKcLV28-25	BGKcLV28-25	BGKcLV28-26	BGKcLV28-26
Sample Name
Sample Name	CMTR1-BGKcLV28-25		CMTR1-BGKcLV28-26
RBP	CMTR1	CMTR1	CMTR1	CMTR1
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2022-01-29	2021-09-16	2022-01-29	2021-09-16
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	9917	9951	9918	9952

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-25	BGKcLV28-26
Sample #	25	26
Sample Name	CMTR1-BGKcLV28-25	CMTR1-BGKcLV28-26
Sample_Name_Alias
Index Well Position	A08	B08
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	323	321
Peak_Molarity	92.60	100.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/A4.png	DNA_Library_set48-49/set3/B4.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set48-49/set2/A4.png	RNA_Library_set48-49/set2/B4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-25	BGKcLV28-26
RBP	CMTR1	CMTR1
Batch_ID	BGKcLV28	BGKcLV28
WB_result	70.200	71.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2086	2087

Sequencing Information

	BGKcLV28-25	BGKcLV28-26
Sample_ID	BGKcLV28-25	BGKcLV28-26
Sample Name	CMTR1-BGKcLV28-25	CMTR1-BGKcLV28-26
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	107,071,442	125,105,852
total_aligned_reads	104,382,826	114,624,490
unique_aligned_reads	95,944,952	105,409,072
percent_uniqueAligned	0.89608	0.84256
correlation_replicates	0.993083	0.993083
spikein_reads	35,872	23,764
percent_spikeins	0.00034	0.00019
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1837	1838

Data Submission Information

	BGKcLV28-25	BGKcLV28-25	BGKcLV28-25	BGKcLV28-25	BGKcLV28-25	BGKcLV28-25	BGKcLV28-26	BGKcLV28-26	BGKcLV28-26	BGKcLV28-26
ENCODE_alias	brenton-graveley:CMTR1-BGKcLV28	brenton-graveley:CMTR1-BGKcLV28-25	brenton-graveley:L-CMTR1-BGKcLV28-25	brenton-graveley:CMTR1-BGKcLV28-25_S107_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CMTR1-BGKcLV28-25_S107_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CMTR1-BGKcLV28-K562	brenton-graveley:CMTR1-BGKcLV28-26	brenton-graveley:L-CMTR1-BGKcLV28-26	brenton-graveley:CMTR1-BGKcLV28-26_S108_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CMTR1-BGKcLV28-26_S108_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR697NDQ	ENCBS050NNR	ENCLB076SAH	ENCFF095ITV	ENCFF318DHS	ENCSR169WSA	ENCBS170BGM	ENCLB868OQW	ENCFF809WNL	ENCFF248BQL
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	BGKcLV28-25	BGKcLV28-25	BGKcLV28-25	BGKcLV28-25	BGKcLV28-25	BGKcLV28-25	BGKcLV28-26	BGKcLV28-26	BGKcLV28-26	BGKcLV28-26
Sample Name	CMTR1-BGKcLV28-25	CMTR1-BGKcLV28-25	CMTR1-BGKcLV28-25	CMTR1-BGKcLV28-25	CMTR1-BGKcLV28-25	CMTR1-BGKcLV28-25	CMTR1-BGKcLV28-26	CMTR1-BGKcLV28-26	CMTR1-BGKcLV28-26	CMTR1-BGKcLV28-26
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		CMTR1-BGKcLV28-25.pdf	L-CMTR1-BGKcLV28-25.pdf				CMTR1-BGKcLV28-26.pdf	L-CMTR1-BGKcLV28-26.pdf
ID	3483	3600	3734	3868	4002	7145	3601	3735	3869	4003

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-BGKcLV28-25_S107_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1837	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	3954
CMTR1-BGKcLV28-25_S107_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1837	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	4012
CMTR1-BGKcLV28-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1837					GRCh38	V40	CMTR1-BGKcLV28-25_S107_L004_R1_001.filtered.trimmed.paired.fastq.gz,CMTR1-BGKcLV28-25_S107_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19236
CMTR1-BGKcLV28-25_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	1837					GRCh38	V40	CMTR1-BGKcLV28-25/Aligned.sortedByCoord.out.bam		ENCORE2	19294
CMTR1-BGKcLV28-25_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	1837					GRCh38	V40	CMTR1-BGKcLV28-25/Aligned.sortedByCoord.out.bam		ENCORE2	19352
CMTR1-BGKcLV28-25_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	1837					GRCh38	V40	CMTR1-BGKcLV28-25/Aligned.sortedByCoord.out.bam		ENCORE2	19410
CMTR1-BGKcLV28-25_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	1837					GRCh38	V40	CMTR1-BGKcLV28-25/Aligned.sortedByCoord.out.bam		ENCORE2	19468
CMTR1-BGKcLV28-25_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1837					GRCh38	V40	CMTR1-BGKcLV28-25_S107_L004_R1_001.filtered.trimmed.paired.fastq.gz,CMTR1-BGKcLV28-25_S107_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19526
CMTR1-BGKcLV28-26_S108_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1838	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	3955
CMTR1-BGKcLV28-26_S108_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1838	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	4013
CMTR1-BGKcLV28-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1838					GRCh38	V40	CMTR1-BGKcLV28-26_S108_L004_R1_001.filtered.trimmed.paired.fastq.gz,CMTR1-BGKcLV28-26_S108_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19237
CMTR1-BGKcLV28-26_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	1838					GRCh38	V40	CMTR1-BGKcLV28-26/Aligned.sortedByCoord.out.bam		ENCORE2	19295
CMTR1-BGKcLV28-26_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	1838					GRCh38	V40	CMTR1-BGKcLV28-26/Aligned.sortedByCoord.out.bam		ENCORE2	19353
CMTR1-BGKcLV28-26_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	1838					GRCh38	V40	CMTR1-BGKcLV28-26/Aligned.sortedByCoord.out.bam		ENCORE2	19411
CMTR1-BGKcLV28-26_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	1838					GRCh38	V40	CMTR1-BGKcLV28-26/Aligned.sortedByCoord.out.bam		ENCORE2	19469
CMTR1-BGKcLV28-26_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1838					GRCh38	V40	CMTR1-BGKcLV28-26_S108_L004_R1_001.filtered.trimmed.paired.fastq.gz,CMTR1-BGKcLV28-26_S108_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19527