EIF3M RNA-Seq in K562

General Information


RBP	EIF3M
Cell_Line	K562
Method	CRISPR
Exp_Name	EIF3M-BGKcLV38-K562
ENCODE_series_ID
Batch_ID	BGKcLV38
Pool ID	Pool-230127C
Local_Set_Name	set56
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF3M-BGKcLV38-57
Rep2	EIF3M-BGKcLV38-58
CN1	NT-BGKcLV38-1
CN2	NT-BGKcLV38-2
Rep1_qPCR	11.7
Rep2_qPCR	24.2
Rep1_WB	53.3
Rep2_WB	50.6
Antibody Cat#	A304-761A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1039

Experiment Information (Status: Submitting)

	BGKcLV38-57	BGKcLV38-58
idx	1474	1475
TRCN#_or_BGC#	BGC#0000977	BGC#0000977
shRNA_or_gRNA_sequence	TTCTTCACTGATGTCGATGA	TTCTTCACTGATGTCGATGA
PAM	AGG	AGG
Name	EIF3M_86	EIF3M_86
Sample_ID	BGKcLV38-57	BGKcLV38-58
transduction_Date	10/18/22	10/18/22
days	D6	D6
RBP_name	EIF3M	EIF3M
qPCR_result	11.7	24.2
Ave_qPCR	18.0
RT-qPCR_primer-F	gcagcaagaacttcagattgg
RT-qPCR_primer-R	tctgggtctgatcaattttgc
protein_conc	3330	3224
WB_result	53.3	50.6
Ave_WB	51.9
WB_DONE_date	11/4/22
MW	43KD
IP
antibody_Cat#	A304-761A	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5658	5659

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF3M	Product_ID: A304-761A Lot_ID: 1 Source: Cell Signaling Technology Target Name: EIF3M-human

Experiment Status

	BGKcLV38-57	BGKcLV38-58
Sample_ID	BGKcLV38-57	BGKcLV38-58
Sample Name
Sample Name	EIF3M-BGKcLV38-57	EIF3M-BGKcLV38-58
RBP	EIF3M	EIF3M
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11052	11053

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV38-57	BGKcLV38-58
Sample #	87	88
Sample Name	EIF3M-BGKcLV38-57	EIF3M-BGKcLV38-58
Sample_Name_Alias
Index Well Position	E12	F12
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-19	2023-01-19
Lib_ID	Lib-230119	Lib-230119
Tecan_Location
Tecan
Tecan_date
Size_bp	292	292
Peak_Molarity	50.50	67.90
libSampleQC_DNA_Well	DNA_Library_set54-56/set2/E12.png	DNA_Library_set54-56/set2/F12.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/G11.png	RNA_Library_set54-56/set1/H11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV38-57	BGKcLV38-58
RBP	EIF3M	EIF3M
Batch_ID	BGKcLV38	BGKcLV38
WB_result	53.300	50.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3458	3459

Sequencing Information

	BGKcLV38-57	BGKcLV38-58
Sample_ID	BGKcLV38-57	BGKcLV38-58
Sample Name	EIF3M-BGKcLV38-57	EIF3M-BGKcLV38-58
Pool ID	Pool-230127C	Pool-230127C
LocalServer_folder	set56	set56
total_reads	46,789,342	73,595,480
total_aligned_reads	43,629,102	70,074,309
unique_aligned_reads	40,530,305	65,024,780
percent_uniqueAligned	0.86623	0.88354
correlation_replicates	0.998034	0.998034
spikein_reads	4,646	10,282
percent_spikeins	0.00010	0.00014
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2329	2330

Data Submission Information DCC submission information was not avaliable

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
EIF3M-BGKcLV38-57_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2329	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8334
EIF3M-BGKcLV38-57_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2329	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8372
EIF3M-BGKcLV38-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2329					GRCh38	V40	EIF3M-BGKcLV38-57_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3M-BGKcLV38-57_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16986
EIF3M-BGKcLV38-57_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2329					GRCh38	V40	EIF3M-BGKcLV38-57/Aligned.sortedByCoord.out.bam		ENCORE2	17024
EIF3M-BGKcLV38-57_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2329					GRCh38	V40	EIF3M-BGKcLV38-57/Aligned.sortedByCoord.out.bam		ENCORE2	17062
EIF3M-BGKcLV38-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2329					GRCh38	V40	EIF3M-BGKcLV38-57/Aligned.sortedByCoord.out.bam		ENCORE2	17100
EIF3M-BGKcLV38-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2329					GRCh38	V40	EIF3M-BGKcLV38-57/Aligned.sortedByCoord.out.bam		ENCORE2	17138
EIF3M-BGKcLV38-57_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2329					GRCh38	V40	EIF3M-BGKcLV38-57_S85_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3M-BGKcLV38-57_S85_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17176
EIF3M-BGKcLV38-58_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2330	NovaSeq6000	100	paired-ended	1				NT-BGKcLV38-1_S51_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8335
EIF3M-BGKcLV38-58_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set56/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2330	NovaSeq6000	100	paired-ended	2				NT-BGKcLV38-1_S51_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV38-2_S52_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8373
EIF3M-BGKcLV38-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2330					GRCh38	V40	EIF3M-BGKcLV38-58_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3M-BGKcLV38-58_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	16987
EIF3M-BGKcLV38-58_Signal.Unique.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2330					GRCh38	V40	EIF3M-BGKcLV38-58/Aligned.sortedByCoord.out.bam		ENCORE2	17025
EIF3M-BGKcLV38-58_Signal.Unique.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2330					GRCh38	V40	EIF3M-BGKcLV38-58/Aligned.sortedByCoord.out.bam		ENCORE2	17063
EIF3M-BGKcLV38-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2330					GRCh38	V40	EIF3M-BGKcLV38-58/Aligned.sortedByCoord.out.bam		ENCORE2	17101
EIF3M-BGKcLV38-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set56/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2330					GRCh38	V40	EIF3M-BGKcLV38-58/Aligned.sortedByCoord.out.bam		ENCORE2	17139
EIF3M-BGKcLV38-58_quant.sf	ENCODE_DATA/set56/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2330					GRCh38	V40	EIF3M-BGKcLV38-58_S86_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF3M-BGKcLV38-58_S86_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17177