EIF2S2 RNA-Seq in HepG2

General Information


RBP	EIF2S2
Cell_Line	HepG2
Method	shRNA
Exp_Name	EIF2S2-BGHLV30-HepG2
ENCODE_series_ID	ENCSR547UVP
Batch_ID	BGHLV30
Pool ID	Pool-151215B
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR110HAA
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	EIF2S2_BGHLV30-31
Rep2	EIF2S2_BGHLV30-32
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	88.7
Rep2_qPCR	89.3
Rep1_WB	66.0
Rep2_WB	59.4
Antibody Cat#	GTX106484
Antibody Lot#	GTX106484
Antibody DCC ID	ENCAB485WQI
Status	Released
Project	ENCODE3
ID	685

Experiment Information (Status: Released)

	BGHLV30-31	BGHLV30-32
idx	717	718
TRCN#_or_BGC#	TRCN0000074788	TRCN0000074788
shRNA_or_gRNA_sequence	GAGTGGATATACCGTTGTATT	GAGTGGATATACCGTTGTATT
PAM
Name	EIF2S2/EIF2B	EIF2S2/EIF2B
Sample_ID	BGHLV30-31	BGHLV30-32
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	EIF2S2	EIF2S2
qPCR_result	88.7	89.3
Ave_qPCR	89.0
RT-qPCR_primer-F	tcaaaggaagattccaacagaaa
RT-qPCR_primer-R	gatcggcatgtgtgacaagt
protein_conc	4356	3993
WB_result	66.0	59.4
Ave_WB	62.7
WB_DONE_date	9/4/2015
MW	38kDa
IP	1	1
antibody_Cat#	GTX106484	GTX106484
Antibody DCC ID	ENCAB485WQI	ENCAB485WQI
submitted_to_DCC_date	12/7/2015
Rep1_TPM	151.3	0
Rep2_TPM	182.4	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2804	2805

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2S2	Product_ID: GTX106484 Lot_ID: 40135 Source: GeneTex Target Name: EIF2S2-human

Experiment Status

	BGHLV30-31	BGHLV30-32
Sample_ID	BGHLV30-31	BGHLV30-32
Sample Name	EIF2S2_BGHLV30-31	EIF2S2_BGHLV30-32
Sample Name	EIF2S2_BGHLV30-31	EIF2S2_BGHLV30-32
RBP	EIF2S2	EIF2S2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1052	1053

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-31	BGHLV30-32
Sample #
Sample Name	EIF2S2-BGHLV30-31	EIF2S2-BGHLV30-32
Sample_Name_Alias	EIF2S2_BGHLV30-31	EIF2S2_BGHLV30-32
Index Well Position	S05	S06
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/E10.png	DNA_Library_LV28-29-30/set1/F10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G5.png	RNA_Library_LV29-30-31-32/set1/H5.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-31	BGHLV30-32
RBP	EIF2S2	EIF2S2
Batch_ID	BGHLV30	BGHLV30
WB_result	66.000	59.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2744	2745

Sequencing Information

	BGHLV30-31	BGHLV30-32
Sample_ID	BGHLV30-31	BGHLV30-32
Sample Name	EIF2S2_BGHLV30-31	EIF2S2_BGHLV30-32
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set30	set30
total_reads	76,581,098	57,196,254
total_aligned_reads	67,765,874	50,791,894
unique_aligned_reads	63,652,372	47,708,122
percent_uniqueAligned	0.83118	0.83411
correlation_replicates	0.999706	0.999706
spikein_reads	202,424	138,592
percent_spikeins	0.00264	0.00242
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1403	1404

Data Submission Information

	BGHLV30-31	BGHLV30-31
ENCODE_alias	brenton-graveley:EIF2S2_BGHLV30	brenton-graveley:EIF2S2-BGHLV30-HepG2
ENCODE_accession	ENCSR110HAA	ENCSR547UVP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-31	BGHLV30-31
Sample Name	EIF2S2_BGHLV30-31	EIF2S2_BGHLV30-31
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3075	6680

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
EIF2S2_BGHLV30-31_ACAGTG_L003_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1403	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20710
EIF2S2_BGHLV30-31_ACAGTG_L003_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1403	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20744
EIF2S2_BGHLV30-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1403					GRCh38	V40	EIF2S2_BGHLV30-31_ACAGTG_L003_001.R1.fastq.gz,EIF2S2_BGHLV30-31_ACAGTG_L003_001.R2.fastq.gz		ENCORE2	20778
EIF2S2_BGHLV30-31_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1403					GRCh38	V40	EIF2S2_BGHLV30-31/Aligned.sortedByCoord.out.bam		ENCORE2	20812
EIF2S2_BGHLV30-31_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1403					GRCh38	V40	EIF2S2_BGHLV30-31/Aligned.sortedByCoord.out.bam		ENCORE2	20846
EIF2S2_BGHLV30-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1403					GRCh38	V40	EIF2S2_BGHLV30-31/Aligned.sortedByCoord.out.bam		ENCORE2	20880
EIF2S2_BGHLV30-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1403					GRCh38	V40	EIF2S2_BGHLV30-31/Aligned.sortedByCoord.out.bam		ENCORE2	20914
EIF2S2_BGHLV30-31_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1403					GRCh38	V40	EIF2S2_BGHLV30-31_ACAGTG_L003_001.R1.fastq.gz,EIF2S2_BGHLV30-31_ACAGTG_L003_001.R2.fastq.gz		ENCORE2	20948
EIF2S2_BGHLV30-32_GCCAAT_L003_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1404	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20711
EIF2S2_BGHLV30-32_GCCAAT_L003_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1404	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20745
EIF2S2_BGHLV30-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1404					GRCh38	V40	EIF2S2_BGHLV30-32_GCCAAT_L003_001.R1.fastq.gz,EIF2S2_BGHLV30-32_GCCAAT_L003_001.R2.fastq.gz		ENCORE2	20779
EIF2S2_BGHLV30-32_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1404					GRCh38	V40	EIF2S2_BGHLV30-32/Aligned.sortedByCoord.out.bam		ENCORE2	20813
EIF2S2_BGHLV30-32_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1404					GRCh38	V40	EIF2S2_BGHLV30-32/Aligned.sortedByCoord.out.bam		ENCORE2	20847
EIF2S2_BGHLV30-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1404					GRCh38	V40	EIF2S2_BGHLV30-32/Aligned.sortedByCoord.out.bam		ENCORE2	20881
EIF2S2_BGHLV30-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1404					GRCh38	V40	EIF2S2_BGHLV30-32/Aligned.sortedByCoord.out.bam		ENCORE2	20915
EIF2S2_BGHLV30-32_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1404					GRCh38	V40	EIF2S2_BGHLV30-32_GCCAAT_L003_001.R1.fastq.gz,EIF2S2_BGHLV30-32_GCCAAT_L003_001.R2.fastq.gz		ENCORE2	20949