EIF2S1 RNA-Seq in HepG2

General Information


RBP	EIF2S1
Cell_Line	HepG2
Method	shRNA
Exp_Name	EIF2S1-BGHLV12-HepG2
ENCODE_series_ID	ENCSR566IBA
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR861ENA
ENCODE_CN_Exp_ID	ENCSR237YZT
Rep1	EIF2S1-BGHLV12-19
Rep2	EIF2S1-BGHLV12-20
CN1	NT-BGHLV12-01
CN2	NT-BGHLV12-02
Rep1_qPCR	64.0
Rep2_qPCR	69.4
Rep1_WB	52.1
Rep2_WB	40.7
Antibody Cat#	A300-721A
Antibody Lot#	A300-721A
Antibody DCC ID	ENCAB888GKD
Status	Released
Project	ENCODE3
ID	334

Experiment Information (Status: Released)

	BGHLV12-19	BGHLV12-20
idx	19	20
TRCN#_or_BGC#	TRCN0000159909	TRCN0000159909
shRNA_or_gRNA_sequence	CGTATCCGTTCTATCAACAAA	CGTATCCGTTCTATCAACAAA
PAM
Name	EIF2S1	EIF2S1
Sample_ID	BGHLV12-19	BGHLV12-20
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	EIF2S1	EIF2S1
qPCR_result	64.0	69.4
Ave_qPCR	66.7
RT-qPCR_primer-F	TATTAATAGGCGCTTGACCC
RT-qPCR_primer-R	GCATCAATGCCTTCATAACCA
protein_conc	3768	3450
WB_result	52.1	40.7
Ave_WB	46.4
WB_DONE_date
MW	36kDa
IP	1	1
antibody_Cat#	A300-721A	A300-721A
Antibody DCC ID	ENCAB888GKD	ENCAB888GKD
submitted_to_DCC_date	4/2/2015
Rep1_TPM	30.5	0
Rep2_TPM	24.4	0
Action
Library_start_date	6/9/2014	6/9/2014
repeat_library
Note
ID	2066	2067

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF2S1	Product_ID: A300-721A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF2S1-human

Experiment Status

	BGHLV12-19	BGHLV12-20
Sample_ID	BGHLV12-19	BGHLV12-20
Sample Name	EIF2S1-BGHLV12-19	EIF2S1-BGHLV12-20
Sample Name	EIF2S1-BGHLV12-19	EIF2S1-BGHLV12-20
RBP	EIF2S1	EIF2S1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	382	383

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-19	BGHLV12-20
Sample #
Sample Name	EIF2S1-BGHLV12-19	EIF2S1-BGHLV12-20
Sample_Name_Alias	EIF2S1-BGHLV12-19	EIF2S1-BGHLV12-20
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-09	2014-06-09
Lib_ID	Lib-140609	Lib-140609
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set1/E2.png	DNA_Library_LV12/set1/F2.png
RIN	9.1	9.3
libSample_RNA_Well	RNA_Library_LV12/set1/E2.png	RNA_Library_LV12/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-19	BGHLV12-20
RBP	EIF2S1	EIF2S1
Batch_ID	BGHLV12	BGHLV12
WB_result	52.100	40.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2004	2005

Sequencing Information

	BGHLV12-19	BGHLV12-20
Sample_ID	BGHLV12-19	BGHLV12-20
Sample Name	EIF2S1-BGHLV12-19	EIF2S1-BGHLV12-20
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	63,600,000	71,290,000
total_aligned_reads	57,678,536	64,284,116
unique_aligned_reads	54,833,562	60,978,934
percent_uniqueAligned	0.86216	0.85536
correlation_replicates	0.998132	0.998132
spikein_reads	475,426	506,254
percent_spikeins	0.00748	0.00710
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	704	705

Data Submission Information

	BGHLV12-19	BGHLV12-19
ENCODE_alias	brenton-graveley:EIF2S1-BGHLV12	brenton-graveley:EIF2S1-BGHLV12-HepG2
ENCODE_accession	ENCSR861ENA	ENCSR566IBA
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-19	BGHLV12-19
Sample Name	EIF2S1-BGHLV12-19	EIF2S1-BGHLV12-19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2740	6678

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
EIF2S1-BGHLV12-19_AGTCAA_L002_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	704	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12761
EIF2S1-BGHLV12-19_AGTCAA_L002_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	704	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12830
EIF2S1-BGHLV12-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	704					GRCh38	V40	EIF2S1-BGHLV12-19_AGTCAA_L002_R1_001.fastq.gz,EIF2S1-BGHLV12-19_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	12900
EIF2S1-BGHLV12-19_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	704					GRCh38	V40	EIF2S1-BGHLV12-19/Aligned.sortedByCoord.out.bam		ENCORE2	12970
EIF2S1-BGHLV12-19_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	704					GRCh38	V40	EIF2S1-BGHLV12-19/Aligned.sortedByCoord.out.bam		ENCORE2	13040
EIF2S1-BGHLV12-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	704					GRCh38	V40	EIF2S1-BGHLV12-19/Aligned.sortedByCoord.out.bam		ENCORE2	13110
EIF2S1-BGHLV12-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	704					GRCh38	V40	EIF2S1-BGHLV12-19/Aligned.sortedByCoord.out.bam		ENCORE2	13180
EIF2S1-BGHLV12-19_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	704					GRCh38	V40	EIF2S1-BGHLV12-19_AGTCAA_L002_R1_001.fastq.gz,EIF2S1-BGHLV12-19_AGTCAA_L002_R2_001.fastq.gz		ENCORE2	13250
EIF2S1-BGHLV12-20_AGTTCC_L002_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	705	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12762
EIF2S1-BGHLV12-20_AGTTCC_L002_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	705	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12831
EIF2S1-BGHLV12-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	705					GRCh38	V40	EIF2S1-BGHLV12-20_AGTTCC_L002_R1_001.fastq.gz,EIF2S1-BGHLV12-20_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	12901
EIF2S1-BGHLV12-20_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	705					GRCh38	V40	EIF2S1-BGHLV12-20/Aligned.sortedByCoord.out.bam		ENCORE2	12971
EIF2S1-BGHLV12-20_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	705					GRCh38	V40	EIF2S1-BGHLV12-20/Aligned.sortedByCoord.out.bam		ENCORE2	13041
EIF2S1-BGHLV12-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	705					GRCh38	V40	EIF2S1-BGHLV12-20/Aligned.sortedByCoord.out.bam		ENCORE2	13111
EIF2S1-BGHLV12-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	705					GRCh38	V40	EIF2S1-BGHLV12-20/Aligned.sortedByCoord.out.bam		ENCORE2	13181
EIF2S1-BGHLV12-20_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	705					GRCh38	V40	EIF2S1-BGHLV12-20_AGTTCC_L002_R1_001.fastq.gz,EIF2S1-BGHLV12-20_AGTTCC_L002_R2_001.fastq.gz		ENCORE2	13251