FIP1L1 RNA-Seq in HepG2

General Information


RBP	FIP1L1
Cell_Line	HepG2
Method	shRNA
Exp_Name	FIP1L1-BGHLV30-HepG2
ENCODE_series_ID	ENCSR563NSV
Batch_ID	BGHLV30
Pool ID	Pool-151215A
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR116QBU
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	FIP1L1_BGHLV30-39
Rep2	FIP1L1_BGHLV30-40
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	57.5
Rep2_qPCR	66.0
Rep1_WB	50.9
Rep2_WB	49.2
Antibody Cat#	A301-461A
Antibody Lot#	A301-461A
Antibody DCC ID	ENCAB786ENG
Status	Released
Project	ENCODE3
ID	679

Experiment Information (Status: Released)

	BGHLV30-39	BGHLV30-39	BGHLV30-40	BGHLV30-40
idx	725	727	726	728
TRCN#_or_BGC#	TRCN0000074418	TRCN0000074418	TRCN0000074418	TRCN0000074418
shRNA_or_gRNA_sequence	GTACCAGAAGTAGATACTATA	GTACCAGAAGTAGATACTATA	GTACCAGAAGTAGATACTATA	GTACCAGAAGTAGATACTATA
PAM
Name	FIP1L1	FIP1L1	FIP1L1	FIP1L1
Sample_ID	BGHLV30-39	BGHLV30-39	BGHLV30-40	BGHLV30-40
transduction_Date	8/25/2015	8/25/2015	8/25/2015	8/25/2015
days
RBP_name	FIP1L1	FIP1L1	FIP1L1	FIP1L1
qPCR_result	57.5	57.5	66.0	66.0
Ave_qPCR	61.8	61.8
RT-qPCR_primer-F	cgggacagagaaagagaacg	cgggacagagaaagagaacg
RT-qPCR_primer-R	tcgctgttgaaaacacttgg	tcgctgttgaaaacacttgg
protein_conc	4061	4061	4093	4093
WB_result	50.9	82.0	49.2	80.8
Ave_WB	50.1	81.4
WB_DONE_date	9/16/2015	12/3/2015
MW	67kDa	67kDa
IP	1	Fu's	1
antibody_Cat#	A301-461A	#A5016	A301-461A	#A5016
Antibody DCC ID	ENCAB786ENG	ENCAB511DBP	ENCAB786ENG	ENCAB511DBP
submitted_to_DCC_date	12/7/2015	12/7/2015
Rep1_TPM	9.8	9.8	0	0
Rep2_TPM	8.1	8.1	0	0
Action
Library_start_date	11/5/2015		11/5/2015
repeat_library
Note	x		x
ID	2812	2814	2813	2815

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FIP1L1	Product_ID: A5016 Lot_ID: unknown Source: ABclonal Target Name: FIP1L1-human
FIP1L1	Product_ID: A301-461A Lot_ID: 1 Source: Bethyl Labs Target Name: FIP1L1-human

Experiment Status

	BGHLV30-39	BGHLV30-40
Sample_ID	BGHLV30-39	BGHLV30-40
Sample Name	FIP1L1_BGHLV30-39	FIP1L1_BGHLV30-40
Sample Name	FIP1L1_BGHLV30-39	FIP1L1_BGHLV30-40
RBP	FIP1L1	FIP1L1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1056	1057

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-39	BGHLV30-40
Sample #
Sample Name	FIP1L1-BGHLV30-39	FIP1L1-BGHLV30-40
Sample_Name_Alias	FIP1L1_BGHLV30-39	FIP1L1_BGHLV30-40
Index Well Position	S09	S10
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/A11.png	DNA_Library_LV28-29-30/set1/B11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C6.png	RNA_Library_LV29-30-31-32/set1/D6.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-39	BGHLV30-40
RBP	FIP1L1	FIP1L1
Batch_ID	BGHLV30	BGHLV30
WB_result	50.900	49.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2748	2749

Sequencing Information

	BGHLV30-39	BGHLV30-40
Sample_ID	BGHLV30-39	BGHLV30-40
Sample Name	FIP1L1_BGHLV30-39	FIP1L1_BGHLV30-40
Pool ID	Pool-151215A	Pool-151215A
LocalServer_folder	set30	set30
total_reads	84,531,962	193,927,736
total_aligned_reads	67,433,930	154,449,114
unique_aligned_reads	63,010,044	144,045,872
percent_uniqueAligned	0.74540	0.74278
correlation_replicates	0.996526	0.996526
spikein_reads	210,388	436,552
percent_spikeins	0.00249	0.00225
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1368	1369

Data Submission Information

	BGHLV30-39	BGHLV30-39
ENCODE_alias	brenton-graveley:FIP1L1_BGHLV30	brenton-graveley:FIP1L1-BGHLV30-HepG2
ENCODE_accession	ENCSR116QBU	ENCSR563NSV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-39	BGHLV30-39
Sample Name	FIP1L1_BGHLV30-39	FIP1L1_BGHLV30-39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3077	6711

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
FIP1L1_BGHLV30-39_GATCAG_L002_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1368	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20714
FIP1L1_BGHLV30-39_GATCAG_L002_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1368	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20748
FIP1L1_BGHLV30-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1368					GRCh38	V40	FIP1L1_BGHLV30-39_GATCAG_L002_001.R1.fastq.gz,FIP1L1_BGHLV30-39_GATCAG_L002_001.R2.fastq.gz		ENCORE2	20782
FIP1L1_BGHLV30-39_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	1368					GRCh38	V40	FIP1L1_BGHLV30-39/Aligned.sortedByCoord.out.bam		ENCORE2	20816
FIP1L1_BGHLV30-39_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	1368					GRCh38	V40	FIP1L1_BGHLV30-39/Aligned.sortedByCoord.out.bam		ENCORE2	20850
FIP1L1_BGHLV30-39_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	1368					GRCh38	V40	FIP1L1_BGHLV30-39/Aligned.sortedByCoord.out.bam		ENCORE2	20884
FIP1L1_BGHLV30-39_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	1368					GRCh38	V40	FIP1L1_BGHLV30-39/Aligned.sortedByCoord.out.bam		ENCORE2	20918
FIP1L1_BGHLV30-39_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1368					GRCh38	V40	FIP1L1_BGHLV30-39_GATCAG_L002_001.R1.fastq.gz,FIP1L1_BGHLV30-39_GATCAG_L002_001.R2.fastq.gz		ENCORE2	20952
FIP1L1_BGHLV30-40_TAGCTT_L002_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1369	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20715
FIP1L1_BGHLV30-40_TAGCTT_L002_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1369	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20749
FIP1L1_BGHLV30-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1369					GRCh38	V40	FIP1L1_BGHLV30-40_TAGCTT_L002_001.R1.fastq.gz,FIP1L1_BGHLV30-40_TAGCTT_L002_001.R2.fastq.gz		ENCORE2	20783
FIP1L1_BGHLV30-40_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	1369					GRCh38	V40	FIP1L1_BGHLV30-40/Aligned.sortedByCoord.out.bam		ENCORE2	20817
FIP1L1_BGHLV30-40_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	1369					GRCh38	V40	FIP1L1_BGHLV30-40/Aligned.sortedByCoord.out.bam		ENCORE2	20851
FIP1L1_BGHLV30-40_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	1369					GRCh38	V40	FIP1L1_BGHLV30-40/Aligned.sortedByCoord.out.bam		ENCORE2	20885
FIP1L1_BGHLV30-40_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	1369					GRCh38	V40	FIP1L1_BGHLV30-40/Aligned.sortedByCoord.out.bam		ENCORE2	20919
FIP1L1_BGHLV30-40_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1369					GRCh38	V40	FIP1L1_BGHLV30-40_TAGCTT_L002_001.R1.fastq.gz,FIP1L1_BGHLV30-40_TAGCTT_L002_001.R2.fastq.gz		ENCORE2	20953