MTREX RNA-Seq in HepG2

Experiment Information (Status: Released)

	BGHcLV31-3	BGHcLV31-4
idx	919	920
TRCN#_or_BGC#	BGC#0000867	BGC#0000867
shRNA_or_gRNA_sequence	CGAGGGCGACTCGACCACTG	CGAGGGCGACTCGACCACTG
PAM	CGG	CGG
Name	MTREX/SKIV2L2_95	MTREX_95
Sample_ID	BGHcLV31-3	BGHcLV31-4
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	MTREX	MTREX
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	aaatccttctaccagtttcagca
RT-qPCR_primer-R	aatttggcaagctgctgtct
protein_conc	3479	3648
WB_result	83.9	80.5
Ave_WB	82.2
WB_DONE_date	11/10/21
MW	118kd
IP
antibody_Cat#	A300-614A	LOT #3
Antibody DCC ID
submitted_to_DCC_date	1/9/24
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/16/21	12/16/21
repeat_library
Note
ID	7098	7099

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
MTREX	Product_ID: A300-614A Lot_ID: 3 Source: Bethyl Labs Target Name: MTREX-human

Experiment Status

	BGHcLV31-3	BGHcLV31-4
Sample_ID	BGHcLV31-3	BGHcLV31-4
Sample Name
Sample Name	SKIV2L2-BGHcLV31-3	SKIV2L2-BGHcLV31-4
RBP	SKIV2L2	SKIV2L2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10289	10290

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-3	BGHcLV31-4
Sample #	3	4
Sample Name	SKIV2L2-BGHcLV31-3	SKIV2L2-BGHcLV31-4
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-12-16	2021-12-16
Lib_ID	Lib-211216	Lib-211216
Tecan_Location
Tecan
Tecan_date
Size_bp	278	282
Peak_Molarity	66.40	79.80
libSampleQC_DNA_Well	DNA_Library_set52/set1/C8.png	DNA_Library_set52/set1/D8.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set52/set1/C1.png	RNA_Library_set52/set1/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-3	BGHcLV31-4
RBP	SKIV2L2	SKIV2L2
Batch_ID	BGHcLV31	BGHcLV31
WB_result	83.900	80.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3180	3181

Sequencing Information

	BGHcLV31-3	BGHcLV31-4
Sample_ID	BGHcLV31-3	BGHcLV31-4
Sample Name	SKIV2L2-BGHcLV31-3	SKIV2L2-BGHcLV31-4
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	80,721,842	86,745,752
total_aligned_reads	70,487,398	74,984,168
unique_aligned_reads	66,279,238	70,472,828
percent_uniqueAligned	0.82108	0.81241
correlation_replicates	0.998725	0.998725
spikein_reads	8,634	5,364
percent_spikeins	0.00011	0.00006
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1977	1978

Data Submission Information

	BGHcLV31-3	BGHcLV31-3	BGHcLV31-3	BGHcLV31-3	BGHcLV31-3	BGHcLV31-3	BGHcLV31-4	BGHcLV31-4	BGHcLV31-4	BGHcLV31-4
ENCODE_alias	brenton-graveley:SKIV2L2-BGHcLV31	brenton-graveley:SKIV2L2-BGHcLV31-3	brenton-graveley:L-SKIV2L2-BGHcLV31-3	brenton-graveley:SKIV2L2-BGHcLV31-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SKIV2L2-BGHcLV31-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SKIV2L2-BGHcLV31-HepG2	brenton-graveley:SKIV2L2-BGHcLV31-4	brenton-graveley:L-SKIV2L2-BGHcLV31-4	brenton-graveley:SKIV2L2-BGHcLV31-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SKIV2L2-BGHcLV31-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR780UNO	ENCBS994SIY	ENCLB019RTY	ENCFF497BDH	ENCFF461IBG	ENCSR714BYM	ENCBS481PFI	ENCLB182GWK	ENCFF151WSS	ENCFF639CXF
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	BGHcLV31-3	BGHcLV31-3	BGHcLV31-3	BGHcLV31-3	BGHcLV31-3	BGHcLV31-3	BGHcLV31-4	BGHcLV31-4	BGHcLV31-4	BGHcLV31-4
Sample Name	SKIV2L2-BGHcLV31-3	SKIV2L2-BGHcLV31-3	SKIV2L2-BGHcLV31-3	SKIV2L2-BGHcLV31-3	SKIV2L2-BGHcLV31-3	SKIV2L2-BGHcLV31-3	SKIV2L2-BGHcLV31-4	SKIV2L2-BGHcLV31-4	SKIV2L2-BGHcLV31-4	SKIV2L2-BGHcLV31-4
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV52_library_protocol					LV52_library_protocol
protocol_URL			L-SKIV2L2-BGHcLV31-3.pdf					L-SKIV2L2-BGHcLV31-4.pdf
ID	7445	7501	7609	7719	7829	7937	7502	7610	7720	7830

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
SKIV2L2-BGHcLV31-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1977	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6551
SKIV2L2-BGHcLV31-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1977	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6605
SKIV2L2-BGHcLV31-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1977					GRCh38	V40	SKIV2L2-BGHcLV31-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,SKIV2L2-BGHcLV31-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18472
SKIV2L2-BGHcLV31-3_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1977					GRCh38	V40	SKIV2L2-BGHcLV31-3/Aligned.sortedByCoord.out.bam		ENCORE2	18526
SKIV2L2-BGHcLV31-3_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1977					GRCh38	V40	SKIV2L2-BGHcLV31-3/Aligned.sortedByCoord.out.bam		ENCORE2	18580
SKIV2L2-BGHcLV31-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1977					GRCh38	V40	SKIV2L2-BGHcLV31-3/Aligned.sortedByCoord.out.bam		ENCORE2	18634
SKIV2L2-BGHcLV31-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1977					GRCh38	V40	SKIV2L2-BGHcLV31-3/Aligned.sortedByCoord.out.bam		ENCORE2	18688
SKIV2L2-BGHcLV31-3_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1977					GRCh38	V40	SKIV2L2-BGHcLV31-3_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,SKIV2L2-BGHcLV31-3_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18742
SKIV2L2-BGHcLV31-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1978	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6552
SKIV2L2-BGHcLV31-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1978	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6606
SKIV2L2-BGHcLV31-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1978					GRCh38	V40	SKIV2L2-BGHcLV31-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,SKIV2L2-BGHcLV31-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18473
SKIV2L2-BGHcLV31-4_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1978					GRCh38	V40	SKIV2L2-BGHcLV31-4/Aligned.sortedByCoord.out.bam		ENCORE2	18527
SKIV2L2-BGHcLV31-4_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1978					GRCh38	V40	SKIV2L2-BGHcLV31-4/Aligned.sortedByCoord.out.bam		ENCORE2	18581
SKIV2L2-BGHcLV31-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1978					GRCh38	V40	SKIV2L2-BGHcLV31-4/Aligned.sortedByCoord.out.bam		ENCORE2	18635
SKIV2L2-BGHcLV31-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1978					GRCh38	V40	SKIV2L2-BGHcLV31-4/Aligned.sortedByCoord.out.bam		ENCORE2	18689
SKIV2L2-BGHcLV31-4_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1978					GRCh38	V40	SKIV2L2-BGHcLV31-4_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz,SKIV2L2-BGHcLV31-4_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18743