EIF2S1 RNA-Seq in K562

General Information


RBP	EIF2S1
Cell_Line	K562
Method	shRNA
Exp_Name	EIF2S1-BGKLV08-K562
ENCODE_series_ID	ENCSR587XOX
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR546MBH
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	EIF2S1-LV08-19
Rep2	EIF2S1-LV08-20
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	72.7
Rep2_qPCR	78.1
Rep1_WB	20.4
Rep2_WB	26.5
Antibody Cat#	A300-721A
Antibody Lot#	A300-721A
Antibody DCC ID	ENCAB888GKD
Status	Released
Project	ENCODE3
ID	286

Experiment Information (Status: Released)

	BGKLV08-19	BGKLV08-20
idx	20	21
TRCN#_or_BGC#	TRCN0000159909	TRCN0000159909
shRNA_or_gRNA_sequence	CGTATCCGTTCTATCAACAAA	CGTATCCGTTCTATCAACAAA
PAM
Name	EIF2S1	EIF2S1
Sample_ID	BGKLV08-19	BGKLV08-20
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	EIF2S1	EIF2S1
qPCR_result	72.7	78.1
Ave_qPCR	75.4
RT-qPCR_primer-F	TATTAATAGGCGCTTGACCC
RT-qPCR_primer-R	GCATCAATGCCTTCATAACCA
protein_conc	2498	2494
WB_result	20.4	26.5
Ave_WB	23.5	NO SAMPLES
WB_DONE_date
MW
IP	1	1
antibody_Cat#	A300-721A	A300-721A
Antibody DCC ID	ENCAB888GKD	ENCAB888GKD
submitted_to_DCC_date	4/2/2015
Rep1_TPM	32.3732499	0
Rep2_TPM	17.9751054	0
Action	Ready	Ready
Library_start_date	5/5/2014	5/5/2014
repeat_library
Note
ID	19	20

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

	BGKLV08-19	BGKLV08-20
Sample_ID	BGKLV08-19	BGKLV08-20
Sample Name	EIF2S1-LV08-19	EIF2S1-LV08-20
Sample Name	EIF2S1-LV08-19	EIF2S1-LV08-20
RBP	EIF2S1	EIF2S1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	280	281

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-19	BGKLV08-20
Sample #
Sample Name	EIF2S1-BGKLV08-19	EIF2S1-BGKLV08-20
Sample_Name_Alias	EIF2S1-LV08-19	EIF2S1-LV08-20
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-05	2014-05-05
Lib_ID	Lib-140505	Lib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set1/H2.png	DNA_Library_LV08/set2/B1.png
RIN	9.2	9.3
libSample_RNA_Well	RNA_Library_LV08/set2/C1.png	RNA_Library_LV08/set2/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-19	BGKLV08-20
RBP	EIF2S1	EIF2S1
Batch_ID	BGKLV08	BGKLV08
WB_result	20.400	26.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1902	1903

Sequencing Information

	BGKLV08-19	BGKLV08-20
Sample_ID	BGKLV08-19	BGKLV08-20
Sample Name	EIF2S1-LV08-19	EIF2S1-LV08-20
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	59,390,000	51,250,000
total_aligned_reads	52,220,938	44,559,004
unique_aligned_reads	47,567,100	40,565,346
percent_uniqueAligned	0.80093	0.79152
correlation_replicates	0.998666	0.998666
spikein_reads	399,010	441,848
percent_spikeins	0.00672	0.00862
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	602	603

Data Submission Information

	BGKLV08-19	BGKLV08-19
ENCODE_alias	brenton-graveley:EIF2S1-LV08	brenton-graveley:EIF2S1-BGKLV08-K562
ENCODE_accession	ENCSR546MBH	ENCSR587XOX
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-19	BGKLV08-19
Sample Name	EIF2S1-LV08-19	EIF2S1-LV08-19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2689	6679

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-LV08-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	602					GRCh38	V40	EIF2S1-LV08-19_ATGTCA_L003_R1_001.fastq.gz,EIF2S1-LV08-19_ATGTCA_L003_R2_001.fastq.gz		ENCORE2	11987
EIF2S1-LV08-19_ATGTCA_L003_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	602	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12043
EIF2S1-LV08-19_ATGTCA_L003_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	602	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12099
EIF2S1-LV08-19_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	602					GRCh38	V40	EIF2S1-LV08-19/Aligned.sortedByCoord.out.bam		ENCORE2	12155
EIF2S1-LV08-19_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	602					GRCh38	V40	EIF2S1-LV08-19/Aligned.sortedByCoord.out.bam		ENCORE2	12211
EIF2S1-LV08-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	602					GRCh38	V40	EIF2S1-LV08-19/Aligned.sortedByCoord.out.bam		ENCORE2	12267
EIF2S1-LV08-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	602					GRCh38	V40	EIF2S1-LV08-19/Aligned.sortedByCoord.out.bam		ENCORE2	12323
EIF2S1-LV08-19_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	602					GRCh38	V40	EIF2S1-LV08-19_ATGTCA_L003_R1_001.fastq.gz,EIF2S1-LV08-19_ATGTCA_L003_R2_001.fastq.gz		ENCORE2	13322
EIF2S1-LV08-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	603					GRCh38	V40	EIF2S1-LV08-20_CCGTCC_L003_R1_001.fastq.gz,EIF2S1-LV08-20_CCGTCC_L003_R2_001.fastq.gz		ENCORE2	11988
EIF2S1-LV08-20_CCGTCC_L003_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	603	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12044
EIF2S1-LV08-20_CCGTCC_L003_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	603	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12100
EIF2S1-LV08-20_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	603					GRCh38	V40	EIF2S1-LV08-20/Aligned.sortedByCoord.out.bam		ENCORE2	12156
EIF2S1-LV08-20_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	603					GRCh38	V40	EIF2S1-LV08-20/Aligned.sortedByCoord.out.bam		ENCORE2	12212
EIF2S1-LV08-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	603					GRCh38	V40	EIF2S1-LV08-20/Aligned.sortedByCoord.out.bam		ENCORE2	12268
EIF2S1-LV08-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	603					GRCh38	V40	EIF2S1-LV08-20/Aligned.sortedByCoord.out.bam		ENCORE2	12324
EIF2S1-LV08-20_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	603					GRCh38	V40	EIF2S1-LV08-20_CCGTCC_L003_R1_001.fastq.gz,EIF2S1-LV08-20_CCGTCC_L003_R2_001.fastq.gz		ENCORE2	13323