EIF2B3 RNA-Seq in HepG2

General Information


RBP	EIF2B3
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF2B3-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR907KNM
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR312UYN
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	EIF2B3-BGHcLV16-23
Rep2	EIF2B3-BGHcLV16-24
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	19.9
Rep2_qPCR	0.0
Rep1_WB	71.0
Rep2_WB	74.1
Antibody Cat#	MA1-078
Antibody Lot#	LOT# NL176595
Antibody DCC ID	ENCAB985GAJ
Status	Released
Project	ENCODE4
ID	148

Experiment Information (Status: Released)

	BGHcLV16-23	BGHcLV16-24
idx	451	452
TRCN#_or_BGC#	BGC#0000388	BGC#0000388
shRNA_or_gRNA_sequence	AACAGACGTTGCCTTACATG	AACAGACGTTGCCTTACATG
PAM	AGG	AGG
Name	EIF2B gamma_89	EIF2B gamma_89
Sample_ID	BGHcLV16-23	BGHcLV16-24
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	EIF2B3	EIF2B3
qPCR_result	19.9	0.0
Ave_qPCR	9.9
RT-qPCR_primer-F	tggtacccattgaacctgct
RT-qPCR_primer-R	ccttttgaacatccctggtt
protein_conc	5198	4552
WB_result	71.0	74.1
Ave_WB	72.5
WB_DONE_date	4/30/19
MW	58KD
IP	Mouse / Ig
antibody_Cat#	MA1-078	LOT# NL176595
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	23	0
Rep2_TPM	30	0
Action	Ready	Ready
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6600	6601

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2B3	Product_ID: MA1-078 Lot_ID: NL176595 Source: Thermo Fisher Target Name: EIF2B3-human

Experiment Status

	BGHcLV16-23	BGHcLV16-24
Sample_ID	BGHcLV16-23	BGHcLV16-24
Sample Name
Sample Name	EIF2B3-BGHcLV16-23	EIF2B3-BGHcLV16-24
RBP	EIF2B3	EIF2B3
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5415	5416

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-23	BGHcLV16-24
Sample #	49	50
Sample Name	EIF2B3-BGHcLV16-23	EIF2B3-BGHcLV16-24
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	1-G1	1-H1
Tecan	34.85	33.59
Tecan_date	2019-12-10	2019-12-10
Size_bp	277	273
Peak_Molarity	53.90	42.00
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/G1.png	DNA_Library_set43-44/set2/H1.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set43-44/set1/G6.png	RNA_Library_set43-44/set1/H6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-23	BGHcLV16-24
RBP	EIF2B3	EIF2B3
Batch_ID	BGHcLV16	BGHcLV16
WB_result	71.000	74.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	625	626

Sequencing Information

	BGHcLV16-23	BGHcLV16-24
Sample_ID	BGHcLV16-23	BGHcLV16-24
Sample Name	EIF2B3-BGHcLV16-23	EIF2B3-BGHcLV16-24
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	99,803,422	111,912,068
total_aligned_reads	93,966,002	107,430,346
unique_aligned_reads	88,071,424	100,644,108
percent_uniqueAligned	0.88245	0.89931
correlation_replicates	0.999381	0.999381
spikein_reads	155,066	172,384
percent_spikeins	0.00155	0.00154
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	127	128

Data Submission Information

	BGHcLV16-23	BGHcLV16-23	BGHcLV16-23	BGHcLV16-23	BGHcLV16-23	BGHcLV16-23	BGHcLV16-24	BGHcLV16-24	BGHcLV16-24	BGHcLV16-24
ENCODE_alias	brenton-graveley:EIF2B3-BGHcLV16	brenton-graveley:EIF2B3-BGHcLV16-23	brenton-graveley:L-EIF2B3-BGHcLV16-23	brenton-graveley:EIF2B3-BGHcLV16-23_S45_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF2B3-BGHcLV16-23_S45_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF2B3-BGHcLV16-HepG2	brenton-graveley:EIF2B3-BGHcLV16-24	brenton-graveley:L-EIF2B3-BGHcLV16-24	brenton-graveley:EIF2B3-BGHcLV16-24_S46_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF2B3-BGHcLV16-24_S46_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR312UYN	ENCBS691PWT	ENCLB416PXB	ENCFF585CVR	ENCFF969QJR	ENCSR907KNM	ENCBS043TYN	ENCLB498HEN	ENCFF995FKT	ENCFF748HJK
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	BGHcLV16-23	BGHcLV16-23	BGHcLV16-23	BGHcLV16-23	BGHcLV16-23	BGHcLV16-23	BGHcLV16-24	BGHcLV16-24	BGHcLV16-24	BGHcLV16-24
Sample Name	EIF2B3-BGHcLV16-23	EIF2B3-BGHcLV16-23	EIF2B3-BGHcLV16-23	EIF2B3-BGHcLV16-23	EIF2B3-BGHcLV16-23	EIF2B3-BGHcLV16-23	EIF2B3-BGHcLV16-24	EIF2B3-BGHcLV16-24	EIF2B3-BGHcLV16-24	EIF2B3-BGHcLV16-24
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		EIF2B3-BGHcLV16-23.pdf	L-EIF2B3-BGHcLV16-23.pdf				EIF2B3-BGHcLV16-24.pdf	L-EIF2B3-BGHcLV16-24.pdf
ID	4	90	254	420	452	7198	91	255	421	453

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
EIF2B3-BGHcLV16-23_S45_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	127	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5
EIF2B3-BGHcLV16-23_S45_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	127	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	37
EIF2B3-BGHcLV16-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	127					GRCh38	V40	EIF2B3-BGHcLV16-23_S45_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B3-BGHcLV16-23_S45_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24168
EIF2B3-BGHcLV16-23_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	127					GRCh38	V40	EIF2B3-BGHcLV16-23/Aligned.sortedByCoord.out.bam		ENCORE2	24200
EIF2B3-BGHcLV16-23_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	127					GRCh38	V40	EIF2B3-BGHcLV16-23/Aligned.sortedByCoord.out.bam		ENCORE2	24232
EIF2B3-BGHcLV16-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	127					GRCh38	V40	EIF2B3-BGHcLV16-23/Aligned.sortedByCoord.out.bam		ENCORE2	24264
EIF2B3-BGHcLV16-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	127					GRCh38	V40	EIF2B3-BGHcLV16-23/Aligned.sortedByCoord.out.bam		ENCORE2	24296
EIF2B3-BGHcLV16-23_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	127					GRCh38	V40	EIF2B3-BGHcLV16-23_S45_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B3-BGHcLV16-23_S45_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24328
EIF2B3-BGHcLV16-24_S46_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	128	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6
EIF2B3-BGHcLV16-24_S46_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	128	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	38
EIF2B3-BGHcLV16-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	128					GRCh38	V40	EIF2B3-BGHcLV16-24_S46_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B3-BGHcLV16-24_S46_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24169
EIF2B3-BGHcLV16-24_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	128					GRCh38	V40	EIF2B3-BGHcLV16-24/Aligned.sortedByCoord.out.bam		ENCORE2	24201
EIF2B3-BGHcLV16-24_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	128					GRCh38	V40	EIF2B3-BGHcLV16-24/Aligned.sortedByCoord.out.bam		ENCORE2	24233
EIF2B3-BGHcLV16-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	128					GRCh38	V40	EIF2B3-BGHcLV16-24/Aligned.sortedByCoord.out.bam		ENCORE2	24265
EIF2B3-BGHcLV16-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	128					GRCh38	V40	EIF2B3-BGHcLV16-24/Aligned.sortedByCoord.out.bam		ENCORE2	24297
EIF2B3-BGHcLV16-24_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	128					GRCh38	V40	EIF2B3-BGHcLV16-24_S46_R1_001.filtered.trimmed.paired.fastq.gz,EIF2B3-BGHcLV16-24_S46_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24329