EIF2B4 RNA-Seq in HepG2

General Information


RBP	EIF2B4
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF2B4-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	EIF2B4-BGHcLV39-49
Rep2	EIF2B4-BGHcLV39-50
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	40.9
Rep2_qPCR	29.7
Rep1_WB	67.1
Rep2_WB	76.6
Antibody Cat#	A302-983A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1250

Experiment Information (Status: Submitting)

	BGHcLV39-49	BGHcLV39-50
idx	1251	1252
TRCN#_or_BGC#	BGC#0000958	BGC#0000958
shRNA_or_gRNA_sequence	ACGAAGCAGGGCAATACACC	ACGAAGCAGGGCAATACACC
PAM	ggg	ggg
Name	EIF2B4_89	EIF2B4_89
Sample_ID	BGHcLV39-49	BGHcLV39-50
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	EIF2B4	EIF2B4
qPCR_result	40.9	29.7
Ave_qPCR	35.3
RT-qPCR_primer-F	tatctgcagcccaatgtcaa
RT-qPCR_primer-R	cgaccagctggaactttctc
protein_conc	1318	989
WB_result	67.1	76.6
Ave_WB	71.8
WB_DONE_date	7/5/23
MW	58KD
IP
antibody_Cat#	A302-983A	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	7442	7443

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2B4	Product_ID: A302-983A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF2B4-human

Experiment Status

	BGHcLV39-49	BGHcLV39-50
Sample_ID	BGHcLV39-49	BGHcLV39-50
Sample Name
Sample Name	EIF2B4-BGHcLV39-49	EIF2B4-BGHcLV39-50
RBP	EIF2B4	EIF2B4
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11992	11993

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-49	BGHcLV39-50
Sample #	19	20
Sample Name	EIF2B4-BGHcLV39-49	EIF2B4-BGHcLV39-50
Sample_Name_Alias
Index Well Position	C03	D03
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	279	276
Peak_Molarity	52.90	57.90
libSampleQC_DNA_Well	DNA_Library_set63/set1/C11.png	DNA_Library_set63/set1/D11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set63/set1/C11.png	RNA_Library_set63/set1/D11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-49	BGHcLV39-50
RBP	EIF2B4	EIF2B4
Batch_ID	BGHcLV39	BGHcLV39
WB_result	67.100	76.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3762	3763

Sequencing Information

	BGHcLV39-49	BGHcLV39-50
Sample_ID	BGHcLV39-49	BGHcLV39-50
Sample Name	EIF2B4-BGHcLV39-49	EIF2B4-BGHcLV39-50
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	63,771,560	98,202,320
total_aligned_reads	51,074,622	81,804,906
unique_aligned_reads	48,086,882	76,948,521
percent_uniqueAligned	0.75405	0.78357
correlation_replicates	0.999701	0.999701
spikein_reads	98,594	61,822
percent_spikeins	0.00155	0.00063
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2661	2662

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
EIF2B4-BGHcLV39-49_S13_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2661	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	8646
EIF2B4-BGHcLV39-49_S13_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2661	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	8672
EIF2B4-BGHcLV39-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2661					GRCh38	V40	EIF2B4-BGHcLV39-49_S13_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B4-BGHcLV39-49_S13_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9943
EIF2B4-BGHcLV39-49_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	2661					GRCh38	V40	EIF2B4-BGHcLV39-49/Aligned.sortedByCoord.out.bam		ENCORE2	9969
EIF2B4-BGHcLV39-49_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	2661					GRCh38	V40	EIF2B4-BGHcLV39-49/Aligned.sortedByCoord.out.bam		ENCORE2	9995
EIF2B4-BGHcLV39-49_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	2661					GRCh38	V40	EIF2B4-BGHcLV39-49/Aligned.sortedByCoord.out.bam		ENCORE2	10021
EIF2B4-BGHcLV39-49_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	2661					GRCh38	V40	EIF2B4-BGHcLV39-49/Aligned.sortedByCoord.out.bam		ENCORE2	10047
EIF2B4-BGHcLV39-49_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2661					GRCh38	V40	EIF2B4-BGHcLV39-49_S13_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B4-BGHcLV39-49_S13_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10073
EIF2B4-BGHcLV39-50_S14_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2662	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	8647
EIF2B4-BGHcLV39-50_S14_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2662	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	8673
EIF2B4-BGHcLV39-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2662					GRCh38	V40	EIF2B4-BGHcLV39-50_S14_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B4-BGHcLV39-50_S14_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9944
EIF2B4-BGHcLV39-50_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	2662					GRCh38	V40	EIF2B4-BGHcLV39-50/Aligned.sortedByCoord.out.bam		ENCORE2	9970
EIF2B4-BGHcLV39-50_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	2662					GRCh38	V40	EIF2B4-BGHcLV39-50/Aligned.sortedByCoord.out.bam		ENCORE2	9996
EIF2B4-BGHcLV39-50_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	2662					GRCh38	V40	EIF2B4-BGHcLV39-50/Aligned.sortedByCoord.out.bam		ENCORE2	10022
EIF2B4-BGHcLV39-50_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	2662					GRCh38	V40	EIF2B4-BGHcLV39-50/Aligned.sortedByCoord.out.bam		ENCORE2	10048
EIF2B4-BGHcLV39-50_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2662					GRCh38	V40	EIF2B4-BGHcLV39-50_S14_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B4-BGHcLV39-50_S14_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10074