EIF3M RNA-Seq in HepG2

General Information


RBP	EIF3M
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF3M-BGHcLV39-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV39
Pool ID	Pool-230830
Local_Set_Name	set63
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF3M-BGHcLV39-63
Rep2	EIF3M-BGHcLV39-64
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	55.7
Rep2_WB	54.4
Antibody Cat#	A304-761A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1253

Experiment Information (Status: Submitting)

	BGHcLV39-63	BGHcLV39-64
idx	1265	1266
TRCN#_or_BGC#	BGC#0000977	BGC#0000977
shRNA_or_gRNA_sequence	TTCTTCACTGATGTCGATGA	TTCTTCACTGATGTCGATGA
PAM	AGG	AGG
Name	EIF3M_86	EIF3M_86
Sample_ID	BGHcLV39-63	BGHcLV39-64
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	EIF3M	EIF3M
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	tgactggaatctcaccactga
RT-qPCR_primer-R	ccaccatgacttttgaagca
protein_conc	1320	2116
WB_result	55.7	54.4
Ave_WB	55.0
WB_DONE_date	7/5/23
MW	43KD
IP
antibody_Cat#	A304-761A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	9/6/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	7456	7457

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

	BGHcLV39-63	BGHcLV39-64
Sample_ID	BGHcLV39-63	BGHcLV39-64
Sample Name
Sample Name	EIF3M-BGHcLV39-63	EIF3M-BGHcLV39-64
RBP	EIF3M	EIF3M
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11998	11999

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-63	BGHcLV39-64
Sample #	25	26
Sample Name	EIF3M-BGHcLV39-63	EIF3M-BGHcLV39-64
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-08-28	2023-08-28
Lib_ID	Lib-230828	Lib-230828
Tecan_Location
Tecan
Tecan_date
Size_bp	274	266
Peak_Molarity	50.90	50.80
libSampleQC_DNA_Well	DNA_Library_set63/set1/A12.png	DNA_Library_set63/set1/B12.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set63/set1/A12.png	RNA_Library_set63/set1/B12.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-63	BGHcLV39-64
RBP	EIF3M	EIF3M
Batch_ID	BGHcLV39	BGHcLV39
WB_result	55.700	54.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3768	3769

Sequencing Information

	BGHcLV39-63	BGHcLV39-64
Sample_ID	BGHcLV39-63	BGHcLV39-64
Sample Name	EIF3M-BGHcLV39-63	EIF3M-BGHcLV39-64
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	15,451,029	82,152,910
total_aligned_reads	11,980,854	65,797,147
unique_aligned_reads	11,271,024	61,895,448
percent_uniqueAligned	0.72947	0.75342
correlation_replicates	0.999021	0.999021
spikein_reads	25,710	103,062
percent_spikeins	0.00166	0.00125
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2667	2668

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-BGHcLV39-63_S500_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2667	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8652
EIF3M-BGHcLV39-63_S500_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2667	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8678
EIF3M-BGHcLV39-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2667					GRCh38	V40	EIF3M-BGHcLV39-63_S500_L004_R1_001.filtered.trimmed.paired.fastq.gz,EIF3M-BGHcLV39-63_S500_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9949
EIF3M-BGHcLV39-63_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2667					GRCh38	V40	EIF3M-BGHcLV39-63/Aligned.sortedByCoord.out.bam		ENCORE2	9975
EIF3M-BGHcLV39-63_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2667					GRCh38	V40	EIF3M-BGHcLV39-63/Aligned.sortedByCoord.out.bam		ENCORE2	10001
EIF3M-BGHcLV39-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2667					GRCh38	V40	EIF3M-BGHcLV39-63/Aligned.sortedByCoord.out.bam		ENCORE2	10027
EIF3M-BGHcLV39-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2667					GRCh38	V40	EIF3M-BGHcLV39-63/Aligned.sortedByCoord.out.bam		ENCORE2	10053
EIF3M-BGHcLV39-63_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2667					GRCh38	V40	EIF3M-BGHcLV39-63_S500_L004_R1_001.filtered.trimmed.paired.fastq.gz,EIF3M-BGHcLV39-63_S500_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10079
EIF3M-BGHcLV39-64_S19_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2668	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8653
EIF3M-BGHcLV39-64_S19_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2668	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8679
EIF3M-BGHcLV39-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2668					GRCh38	V40	EIF3M-BGHcLV39-64_S19_R1_001.filtered.trimmed.paired.fastq.gz,EIF3M-BGHcLV39-64_S19_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9950
EIF3M-BGHcLV39-64_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2668					GRCh38	V40	EIF3M-BGHcLV39-64/Aligned.sortedByCoord.out.bam		ENCORE2	9976
EIF3M-BGHcLV39-64_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2668					GRCh38	V40	EIF3M-BGHcLV39-64/Aligned.sortedByCoord.out.bam		ENCORE2	10002
EIF3M-BGHcLV39-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2668					GRCh38	V40	EIF3M-BGHcLV39-64/Aligned.sortedByCoord.out.bam		ENCORE2	10028
EIF3M-BGHcLV39-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2668					GRCh38	V40	EIF3M-BGHcLV39-64/Aligned.sortedByCoord.out.bam		ENCORE2	10054
EIF3M-BGHcLV39-64_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2668					GRCh38	V40	EIF3M-BGHcLV39-64_S19_R1_001.filtered.trimmed.paired.fastq.gz,EIF3M-BGHcLV39-64_S19_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10080