NUFIP2 RNA-Seq in HepG2

General Information


RBP	NUFIP2
Cell_Line	HepG2
Method	shRNA
Exp_Name	NUFIP2-BGHLV26-HepG2
ENCODE_series_ID	ENCSR804FLV
Batch_ID	BGHLV26
Pool ID	Pool-151201
Local_Set_Name	set26
ENCODE_KD_Exp_ID	ENCSR584JRB
ENCODE_CN_Exp_ID	ENCSR104ABF
Rep1	NUFIP2_BGHLV26_29
Rep2	NUFIP2_BGHLV26_30
CN1	non-target_BGHLV26-1
CN2	non-target_BGHLV26-2
Rep1_qPCR	54.6
Rep2_qPCR	50.0
Rep1_WB	70.7
Rep2_WB	77.1
Antibody Cat#	A301-599A
Antibody Lot#	A301-599A
Antibody DCC ID	ENCAB072KYE
Status	Released
Project	ENCODE3
ID	631

Experiment Information (Status: Released)

	BGHLV26-29	BGHLV26-30
idx	585	586
TRCN#_or_BGC#	TRCN0000167367	TRCN0000167367
shRNA_or_gRNA_sequence	GAAACTTTCAAGCCTGACTAT	GAAACTTTCAAGCCTGACTAT
PAM
Name	NUFIP2	NUFIP2
Sample_ID	BGHLV26-29	BGHLV26-30
transduction_Date	5/25/2015	5/25/2015
days
RBP_name	NUFIP2	NUFIP2
qPCR_result	54.6	50.0
Ave_qPCR	52.3
RT-qPCR_primer-F	tggaatttgcagaagcaaga
RT-qPCR_primer-R	tctggtccttcattgatctgg
protein_conc	5260	4900
WB_result	70.7	77.1
Ave_WB	73.9
WB_DONE_date	7/27/2015
MW	76kDa
IP	1	1
antibody_Cat#	A301-599A	A301-599A
Antibody DCC ID	ENCAB072KYE	ENCAB072KYE
submitted_to_DCC_date	8/6/2015
Rep1_TPM	8.5	0
Rep2_TPM	9.7	0
Action
Library_start_date	9/8/2015	9/8/2015
repeat_library
Note	x	x
ID	2668	2669

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NUFIP2	Product_ID: A301-599A Lot_ID: 1 Source: Bethyl Labs Target Name: NUFIP2-human

Experiment Status

	BGHLV26-29	BGHLV26-30
Sample_ID	BGHLV26-29	BGHLV26-30
Sample Name	NUFIP2_BGHLV26_29	NUFIP2_BGHLV26_30
Sample Name	NUFIP2_BGHLV26_29	NUFIP2_BGHLV26_30
RBP	NUFIP2	NUFIP2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-01-16	2016-01-16
Project	ENCODE3	ENCODE3
Note
ID	946	947

Library-Prep
Sequencing

Library-Prep Information

	BGHLV26-29	BGHLV26-30
Sample #
Sample Name	NUFIP2-BGHLV26-29	NUFIP2-BGHLV26-30
Sample_Name_Alias	NUFIP2_BGHLV26_29	NUFIP2_BGHLV26_30
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-08	2015-09-08
Lib_ID	Lib-150908	Lib-150908
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/G8.png	DNA_Library_LV24-25-26/set2/G2.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_LV25-26/set1/A2.png	RNA_Library_LV25-26/set1/B2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV26-29	BGHLV26-30
RBP	NUFIP2	NUFIP2
Batch_ID	BGHLV26	BGHLV26
WB_result	70.700	77.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2634	2635

Sequencing Information

	BGHLV26-29	BGHLV26-30
Sample_ID	BGHLV26-29	BGHLV26-30
Sample Name	NUFIP2_BGHLV26_29	NUFIP2_BGHLV26_30
Pool ID	Pool-151201	Pool-151201
LocalServer_folder	set26	set26
total_reads	85,979,444	83,206,326
total_aligned_reads	73,326,012	72,389,754
unique_aligned_reads	68,575,100	67,827,156
percent_uniqueAligned	0.79758	0.81517
correlation_replicates	0.992542	0.992542
spikein_reads	197,138	169,104
percent_spikeins	0.00229	0.00203
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1276	1277

Data Submission Information

	BGHLV26-29	BGHLV26-29
ENCODE_alias	brenton-graveley:NUFIP2_BGHLV26	brenton-graveley:NUFIP2-BGHLV26-HepG2
ENCODE_accession	ENCSR584JRB	ENCSR804FLV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV26-29	BGHLV26-29
Sample Name	NUFIP2_BGHLV26_29	NUFIP2_BGHLV26_29
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-01-14	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3020	6834

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
NUFIP2_BGHLV26_29_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1276	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19820
NUFIP2_BGHLV26_29_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1276	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19842
NUFIP2_BGHLV26_29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1276					GRCh38	V40	NUFIP2_BGHLV26_29_1.fastq.gz,NUFIP2_BGHLV26_29_2.fastq.gz		ENCORE2	19864
NUFIP2_BGHLV26_29_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1276					GRCh38	V40	NUFIP2_BGHLV26_29/Aligned.sortedByCoord.out.bam		ENCORE2	19886
NUFIP2_BGHLV26_29_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1276					GRCh38	V40	NUFIP2_BGHLV26_29/Aligned.sortedByCoord.out.bam		ENCORE2	19908
NUFIP2_BGHLV26_29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1276					GRCh38	V40	NUFIP2_BGHLV26_29/Aligned.sortedByCoord.out.bam		ENCORE2	19930
NUFIP2_BGHLV26_29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1276					GRCh38	V40	NUFIP2_BGHLV26_29/Aligned.sortedByCoord.out.bam		ENCORE2	19952
NUFIP2_BGHLV26_29_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1276					GRCh38	V40	NUFIP2_BGHLV26_29_1.fastq.gz,NUFIP2_BGHLV26_29_2.fastq.gz		ENCORE2	20660
NUFIP2_BGHLV26_30_1.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1277	HiSeq2500	100	paired-ended	1				non-target_BGHLV26-1_1.fastq.gz,non-target_BGHLV26-2_1.fastq.gz	ENCODE3	19821
NUFIP2_BGHLV26_30_2.fastq.gz	ENCODE_DATA/set26/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1277	HiSeq2500	100	paired-ended	2				non-target_BGHLV26-1_2.fastq.gz,non-target_BGHLV26-2_2.fastq.gz	ENCODE3	19843
NUFIP2_BGHLV26_30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1277					GRCh38	V40	NUFIP2_BGHLV26_30_1.fastq.gz,NUFIP2_BGHLV26_30_2.fastq.gz		ENCORE2	19865
NUFIP2_BGHLV26_30_Signal.Unique.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1277					GRCh38	V40	NUFIP2_BGHLV26_30/Aligned.sortedByCoord.out.bam		ENCORE2	19887
NUFIP2_BGHLV26_30_Signal.Unique.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1277					GRCh38	V40	NUFIP2_BGHLV26_30/Aligned.sortedByCoord.out.bam		ENCORE2	19909
NUFIP2_BGHLV26_30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1277					GRCh38	V40	NUFIP2_BGHLV26_30/Aligned.sortedByCoord.out.bam		ENCORE2	19931
NUFIP2_BGHLV26_30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set26/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1277					GRCh38	V40	NUFIP2_BGHLV26_30/Aligned.sortedByCoord.out.bam		ENCORE2	19953
NUFIP2_BGHLV26_30_quant.sf	ENCODE_DATA/set26/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1277					GRCh38	V40	NUFIP2_BGHLV26_30_1.fastq.gz,NUFIP2_BGHLV26_30_2.fastq.gz		ENCORE2	20661