MTREX RNA-Seq in K562

Experiment Information (Status: Released)

	BGKcLV33-49	BGKcLV33-49	BGKcLV33-50	BGKcLV33-50
idx	1151	1238	1152	1239
TRCN#_or_BGC#	BGC#0000867	BGC#0000862	BGC#0000867	BGC#0000862
shRNA_or_gRNA_sequence	CGAGGGCGACTCGACCACTG	TGGACCTGACATGGCAACGG	CGAGGGCGACTCGACCACTG	TGGACCTGACATGGCAACGG
PAM	CGG	GGG	CGG	GGG
Name	MTREX_95	SETD1A_88	MTREX_95	SETD1A_88
Sample_ID	BGKcLV33-49	BGKcLV33-49	BGKcLV33-50	BGKcLV33-50
transduction_Date	12/7/21	2/22/22	12/7/21	2/22/22
days	D6	D6	D6	D6
RBP_name	MTREX	SETD1A	MTREX	SETD1A
qPCR_result		0.0		0.0
Ave_qPCR		0.0
RT-qPCR_primer-F		gaaacggtcaaaaacctcca
RT-qPCR_primer-R		gggtgtaggagccattgaca
protein_conc	322	2298	415	2151
WB_result	85.7	56.5	91.9	55.1
Ave_WB	88.8	55.8
WB_DONE_date	2/3/22	3/24/22
MW	118kd	186kd
IP
antibody_Cat#	A300-614A	A300-290A	LOT #3	LOT #2
Antibody DCC ID		ENCAB028FFK		8/4/22
submitted_to_DCC_date		8/16/23
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action		Ready		Ready
Library_start_date		04/13/22		04/13/22
repeat_library
Note
ID	5291	5380	5292	5381

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SETD1A	Product_ID: A300-290A Lot_ID: 2 Source: Bethyl Labs Target Name: SETD1A-human

Experiment Status

	BGKcLV33-49	BGKcLV33-49	BGKcLV33-50	BGKcLV33-50
Sample_ID	BGKcLV33-49	BGKcLV33-49	BGKcLV33-50	BGKcLV33-50
Sample Name
Sample Name	SETD1A-BGKcLV33-49		SETD1A-BGKcLV33-50
RBP	SETD1A	SKIV2L2	SETD1A	SKIV2L2
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2022-10-28	2022-03-30	2022-10-28	2022-03-30
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	10665	10735	10666	10736

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV33-49	BGKcLV33-50
Sample #	35	36
Sample Name	SETD1A-BGKcLV33-49	SETD1A-BGKcLV33-50
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-04-06	2022-04-06
Lib_ID	Lib-220406	Lib-220406
Tecan_Location
Tecan
Tecan_date
Size_bp	288	301
Peak_Molarity	60.40	52.30
libSampleQC_DNA_Well	DNA_Library_set53/set1/C9.png	DNA_Library_set53/set1/D9.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set53/set1/C5.png	RNA_Library_set53/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-04-18	2022-04-18
Sample_ID	BGKcLV33-49	BGKcLV33-50
RBP	SETD1A	SETD1A
Batch_ID	BGKcLV33	BGKcLV33
WB_result	56.527	55.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3296	3297

Sequencing Information

	BGKcLV33-49	BGKcLV33-50
Sample_ID	BGKcLV33-49	BGKcLV33-50
Sample Name	SETD1A-BGKcLV33-49	SETD1A-BGKcLV33-50
Pool ID	Pool-220418	Pool-220418
LocalServer_folder	set53	set53
total_reads	109,608,204	75,750,746
total_aligned_reads	99,717,720	70,156,550
unique_aligned_reads	91,096,450	64,046,646
percent_uniqueAligned	0.83111	0.84549
correlation_replicates	0.993355	0.993355
spikein_reads	11,978	4,498
percent_spikeins	0.00011	0.00006
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2063	2064

Data Submission Information

	BGKcLV33-49	BGKcLV33-49	BGKcLV33-49	BGKcLV33-49	BGKcLV33-49	BGKcLV33-49	BGKcLV33-50	BGKcLV33-50	BGKcLV33-50	BGKcLV33-50
ENCODE_alias	brenton-graveley:SETD1A-BGKcLV33	brenton-graveley:SETD1A-BGKcLV33-49	brenton-graveley:L-SETD1A-BGKcLV33-49	brenton-graveley:SETD1A-BGKcLV33-49_S89_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SETD1A-BGKcLV33-49_S89_L002_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SETD1A-BGKcLV33-K562	brenton-graveley:SETD1A-BGKcLV33-50	brenton-graveley:L-SETD1A-BGKcLV33-50	brenton-graveley:SETD1A-BGKcLV33-50_S90_L002_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SETD1A-BGKcLV33-50_S90_L002_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR558XPA	ENCBS202NAP	ENCLB164VBO	ENCFF571KVK	ENCFF516DIG	ENCSR438ODL	ENCBS754IVU	ENCLB985NHG	ENCFF813PQZ	ENCFF003TPP
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	BGKcLV33-49	BGKcLV33-49	BGKcLV33-49	BGKcLV33-49	BGKcLV33-49	BGKcLV33-49	BGKcLV33-50	BGKcLV33-50	BGKcLV33-50	BGKcLV33-50
Sample Name	SETD1A-BGKcLV33-49	SETD1A-BGKcLV33-49	SETD1A-BGKcLV33-49	SETD1A-BGKcLV33-49	SETD1A-BGKcLV33-49	SETD1A-BGKcLV33-49	SETD1A-BGKcLV33-50	SETD1A-BGKcLV33-50	SETD1A-BGKcLV33-50	SETD1A-BGKcLV33-50
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	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
		LV53_biosample_protocol	LV53_library_protocol				LV53_biosample_protocol	LV53_library_protocol
protocol_URL		SETD1A-BGKcLV33-49.pdf	L-SETD1A-BGKcLV33-49.pdf				SETD1A-BGKcLV33-50.pdf	L-SETD1A-BGKcLV33-50.pdf
ID	7487	7583	7693	7805	7915	7977	7584	7694	7806	7916

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
SETD1A-BGKcLV33-49_S89_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2063	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6641
SETD1A-BGKcLV33-49_S89_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2063	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6697
SETD1A-BGKcLV33-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2063					GRCh38	V40	SETD1A-BGKcLV33-49_S89_L002_R1_001.filtered.trimmed.paired.fastq.gz,SETD1A-BGKcLV33-49_S89_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18118
SETD1A-BGKcLV33-49_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2063					GRCh38	V40	SETD1A-BGKcLV33-49/Aligned.sortedByCoord.out.bam		ENCORE2	18174
SETD1A-BGKcLV33-49_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2063					GRCh38	V40	SETD1A-BGKcLV33-49/Aligned.sortedByCoord.out.bam		ENCORE2	18230
SETD1A-BGKcLV33-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2063					GRCh38	V40	SETD1A-BGKcLV33-49/Aligned.sortedByCoord.out.bam		ENCORE2	18286
SETD1A-BGKcLV33-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2063					GRCh38	V40	SETD1A-BGKcLV33-49/Aligned.sortedByCoord.out.bam		ENCORE2	18342
SETD1A-BGKcLV33-49_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2063					GRCh38	V40	SETD1A-BGKcLV33-49_S89_L002_R1_001.filtered.trimmed.paired.fastq.gz,SETD1A-BGKcLV33-49_S89_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18398
SETD1A-BGKcLV33-50_S90_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2064	NovaSeq6000	100	paired-ended	1				NT-BGKcLV33-1_S55_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6642
SETD1A-BGKcLV33-50_S90_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set53/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2064	NovaSeq6000	100	paired-ended	2				NT-BGKcLV33-1_S55_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV33-2_S56_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6698
SETD1A-BGKcLV33-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2064					GRCh38	V40	SETD1A-BGKcLV33-50_S90_L002_R1_001.filtered.trimmed.paired.fastq.gz,SETD1A-BGKcLV33-50_S90_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18119
SETD1A-BGKcLV33-50_Signal.Unique.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2064					GRCh38	V40	SETD1A-BGKcLV33-50/Aligned.sortedByCoord.out.bam		ENCORE2	18175
SETD1A-BGKcLV33-50_Signal.Unique.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2064					GRCh38	V40	SETD1A-BGKcLV33-50/Aligned.sortedByCoord.out.bam		ENCORE2	18231
SETD1A-BGKcLV33-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2064					GRCh38	V40	SETD1A-BGKcLV33-50/Aligned.sortedByCoord.out.bam		ENCORE2	18287
SETD1A-BGKcLV33-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set53/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2064					GRCh38	V40	SETD1A-BGKcLV33-50/Aligned.sortedByCoord.out.bam		ENCORE2	18343
SETD1A-BGKcLV33-50_quant.sf	ENCODE_DATA/set53/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2064					GRCh38	V40	SETD1A-BGKcLV33-50_S90_L002_R1_001.filtered.trimmed.paired.fastq.gz,SETD1A-BGKcLV33-50_S90_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18399