NELFE RNA-Seq in HepG2

General Information


RBP	NELFE
Cell_Line	HepG2
Method	shRNA
Exp_Name	NELFE-BGHLV12-HepG2
ENCODE_series_ID	ENCSR015WFP
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR939ZRA
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	RDBP-BGHLV12-69
Rep2	RDBP-BGHLV12-70
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	53.7
Rep2_qPCR	62.0
Rep1_WB	98.3
Rep2_WB	97.9
Antibody Cat#	A301-913A
Antibody Lot#	A301-913A
Antibody DCC ID	ENCAB361TEG
Status	Released
Project	ENCODE3
ID	351

Experiment Information (Status: Released)

	BGHLV12-69	BGHLV12-70
idx	69	70
TRCN#_or_BGC#	TRCN0000074958	TRCN0000074958
shRNA_or_gRNA_sequence	CTGGATTCCTTGTGCCTCATA	CTGGATTCCTTGTGCCTCATA
PAM
Name	RDBP	RDBP
Sample_ID	BGHLV12-69	BGHLV12-70
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	NELFE	NELFE
qPCR_result	53.7	62.0
Ave_qPCR	57.9
RT-qPCR_primer-F	AGCAAAGTAGCAGCAGCACA
RT-qPCR_primer-R	GTCTCAGCCTTGATGGCACT
protein_conc	2037	2466
WB_result	98.3	97.9
Ave_WB	98.1
WB_DONE_date	3/19/2015
MW	43kDa
IP	1	1
antibody_Cat#	A301-913A	A301-913A
Antibody DCC ID	ENCAB361TEG	ENCAB361TEG
submitted_to_DCC_date	4/2/2015
Rep1_TPM	32.8	0
Rep2_TPM	29.8	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2122	2123

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NELFE	Product_ID: A301-913A Lot_ID: 1 Source: Bethyl Labs Target Name: NELFE-human

Experiment Status

	BGHLV12-69	BGHLV12-70
Sample_ID	BGHLV12-69	BGHLV12-70
Sample Name	RDBP-BGHLV12-69	RDBP-BGHLV12-70
Sample Name	RDBP-BGHLV12-69	RDBP-BGHLV12-70
RBP	NELFE	NELFE
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	422	423

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-69	BGHLV12-70
Sample #
Sample Name	NELFE-BGHLV12-69	NELFE-BGHLV12-70
Sample_Name_Alias	RDBP-BGHLV12-69	RDBP-BGHLV12-70
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/C3.png	DNA_Library_LV12/set3/D3.png
RIN	9.4	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/C7.png	RNA_Library_LV12/set1/D7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-69	BGHLV12-70
RBP	NELFE	NELFE
Batch_ID	BGHLV12	BGHLV12
WB_result	98.300	97.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2046	2047

Sequencing Information

	BGHLV12-69	BGHLV12-70
Sample_ID	BGHLV12-69	BGHLV12-70
Sample Name	RDBP-BGHLV12-69	RDBP-BGHLV12-70
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	72,390,000	66,760,000
total_aligned_reads	64,678,770	58,927,308
unique_aligned_reads	61,033,634	55,594,078
percent_uniqueAligned	0.84312	0.83275
correlation_replicates	0.997449	0.997449
spikein_reads	292,838	395,848
percent_spikeins	0.00405	0.00593
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	744	745

Data Submission Information

	BGHLV12-69	BGHLV12-69
ENCODE_alias	brenton-graveley:RDBP-BGHLV12	brenton-graveley:NELFE-BGHLV12-HepG2
ENCODE_accession	ENCSR939ZRA	ENCSR015WFP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-69	BGHLV12-69
Sample Name	RDBP-BGHLV12-69	RDBP-BGHLV12-69
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2760	6820

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
RDBP-BGHLV12-69_TTAGGC_L008_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	744	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12805
RDBP-BGHLV12-69_TTAGGC_L008_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	744	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12874
RDBP-BGHLV12-69_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	744					GRCh38	V40	RDBP-BGHLV12-69_TTAGGC_L008_R1_001.fastq.gz,RDBP-BGHLV12-69_TTAGGC_L008_R2_001.fastq.gz		ENCORE2	12944
RDBP-BGHLV12-69_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	744					GRCh38	V40	RDBP-BGHLV12-69/Aligned.sortedByCoord.out.bam		ENCORE2	13014
RDBP-BGHLV12-69_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	744					GRCh38	V40	RDBP-BGHLV12-69/Aligned.sortedByCoord.out.bam		ENCORE2	13084
RDBP-BGHLV12-69_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	744					GRCh38	V40	RDBP-BGHLV12-69/Aligned.sortedByCoord.out.bam		ENCORE2	13154
RDBP-BGHLV12-69_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	744					GRCh38	V40	RDBP-BGHLV12-69/Aligned.sortedByCoord.out.bam		ENCORE2	13224
RDBP-BGHLV12-69_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	744					GRCh38	V40	RDBP-BGHLV12-69_TTAGGC_L008_R1_001.fastq.gz,RDBP-BGHLV12-69_TTAGGC_L008_R2_001.fastq.gz		ENCORE2	13294
RDBP-BGHLV12-70_TGACCA_L008_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	745	HiSeq2000	100	paired-ended	1				NT-BGHLV12-93_GTGGCC_L007_R1_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R1_001.fastq.gz	ENCODE3	12806
RDBP-BGHLV12-70_TGACCA_L008_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	745	HiSeq2000	100	paired-ended	2				NT-BGHLV12-93_GTGGCC_L007_R2_001.fastq.gz,NT-BGHLV12-94_GTTTCG_L007_R2_001.fastq.gz	ENCODE3	12875
RDBP-BGHLV12-70_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	745					GRCh38	V40	RDBP-BGHLV12-70_TGACCA_L008_R1_001.fastq.gz,RDBP-BGHLV12-70_TGACCA_L008_R2_001.fastq.gz		ENCORE2	12945
RDBP-BGHLV12-70_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	745					GRCh38	V40	RDBP-BGHLV12-70/Aligned.sortedByCoord.out.bam		ENCORE2	13015
RDBP-BGHLV12-70_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	745					GRCh38	V40	RDBP-BGHLV12-70/Aligned.sortedByCoord.out.bam		ENCORE2	13085
RDBP-BGHLV12-70_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	745					GRCh38	V40	RDBP-BGHLV12-70/Aligned.sortedByCoord.out.bam		ENCORE2	13155
RDBP-BGHLV12-70_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	745					GRCh38	V40	RDBP-BGHLV12-70/Aligned.sortedByCoord.out.bam		ENCORE2	13225
RDBP-BGHLV12-70_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	745					GRCh38	V40	RDBP-BGHLV12-70_TGACCA_L008_R1_001.fastq.gz,RDBP-BGHLV12-70_TGACCA_L008_R2_001.fastq.gz		ENCORE2	13295