FIP1L1 RNA-Seq in K562

General Information


RBP	FIP1L1
Cell_Line	K562
Method	shRNA
Exp_Name	FIP1L1-BGKLV29-K562
ENCODE_series_ID	ENCSR121BDY
Batch_ID	BGKLV29
Pool ID	Pool-151215B
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR511BNY
ENCODE_CN_Exp_ID	ENCSR032YMP
Rep1	FIP1L1_BGKLV29-33
Rep2	FIP1L1_BGKLV29-34
CN1	NT_BGKLV29-1
CN2	NT_BGKLV29-2
Rep1_qPCR	75.3
Rep2_qPCR	70.3
Rep1_WB	77.3
Rep2_WB	70.0
Antibody Cat#	A301-461A
Antibody Lot#	A301-461A
Antibody DCC ID	ENCAB786ENG
Status	Released
Project	ENCODE3
ID	669

Experiment Information (Status: Released)

	BGKLV29-33	BGKLV29-33	BGKLV29-34	BGKLV29-34
idx	566	568	567	569
TRCN#_or_BGC#	TRCN0000074418	TRCN0000074418	TRCN0000074418	TRCN0000074418
shRNA_or_gRNA_sequence	GTACCAGAAGTAGATACTATA	GTACCAGAAGTAGATACTATA	GTACCAGAAGTAGATACTATA	GTACCAGAAGTAGATACTATA
PAM
Name	FIP1L1_18	FIP1L1_18	FIP1L1_18	FIP1L1_18
Sample_ID	BGKLV29-33	BGKLV29-33	BGKLV29-34	BGKLV29-34
transduction_Date	8/11/2015	8/11/2015	8/11/2015	8/11/2015
days
RBP_name	FIP1L1	FIP1L1	FIP1L1	FIP1L1
qPCR_result	75.3	75.3	70.3	70.3
Ave_qPCR	72.8	72.8
RT-qPCR_primer-F	cgggacagagaaagagaacg	cgggacagagaaagagaacg
RT-qPCR_primer-R	tcgctgttgaaaacacttgg	tcgctgttgaaaacacttgg
protein_conc	3270	0	3185	0
WB_result	77.3	73.6	70.0	75.6
Ave_WB	73.7	74.6	no more samples
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	25.2884553	25.2884553	0	0
Rep2_TPM	23.7477449	23.7477449	0	0
Action
Library_start_date	11/2/2015		11/2/2015
repeat_library
Note	x		x
ID	645	647	646	648

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

	BGKLV29-33	BGKLV29-34
Sample_ID	BGKLV29-33	BGKLV29-34
Sample Name	FIP1L1_BGKLV29-33	FIP1L1_BGKLV29-34
Sample Name	FIP1L1_BGKLV29-33	FIP1L1_BGKLV29-34
RBP	FIP1L1	FIP1L1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1020	1021

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-33	BGKLV29-34
Sample #
Sample Name	FIP1L1-BGKLV29-33	FIP1L1-BGKLV29-34
Sample_Name_Alias	FIP1L1_BGKLV29-33	FIP1L1_BGKLV29-34
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-02	2015-11-02
Lib_ID	Lib-151102	Lib-151102
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/C6.png	DNA_Library_LV28-29-30/set1/D6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G1.png	RNA_Library_LV29-30-31-32/set1/H1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-33	BGKLV29-34
RBP	FIP1L1	FIP1L1
Batch_ID	BGKLV29	BGKLV29
WB_result	77.300	70.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2710	2711

Sequencing Information

	BGKLV29-33	BGKLV29-34
Sample_ID	BGKLV29-33	BGKLV29-34
Sample Name	FIP1L1_BGKLV29-33	FIP1L1_BGKLV29-34
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set29	set29
total_reads	63,829,332	61,759,678
total_aligned_reads	57,586,794	54,140,178
unique_aligned_reads	52,167,586	48,877,768
percent_uniqueAligned	0.81730	0.79142
correlation_replicates	0.998612	0.998612
spikein_reads	372,864	302,160
percent_spikeins	0.00584	0.00489
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1381	1382

Data Submission Information

	BGKLV29-33	BGKLV29-33
ENCODE_alias	brenton-graveley:FIP1L1_BGKLV29	brenton-graveley:FIP1L1-BGKLV29-K562
ENCODE_accession	ENCSR511BNY	ENCSR121BDY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-33	BGKLV29-33
Sample Name	FIP1L1_BGKLV29-33	FIP1L1_BGKLV29-33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3059	6712

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_BGKLV29-33_GTGGCC_L002_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1381	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20422
FIP1L1_BGKLV29-33_GTGGCC_L002_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1381	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20452
FIP1L1_BGKLV29-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1381					GRCh38	V40	FIP1L1_BGKLV29-33_GTGGCC_L002_001.R1.fastq.gz,FIP1L1_BGKLV29-33_GTGGCC_L002_001.R2.fastq.gz		ENCORE2	20482
FIP1L1_BGKLV29-33_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1381					GRCh38	V40	FIP1L1_BGKLV29-33/Aligned.sortedByCoord.out.bam		ENCORE2	20512
FIP1L1_BGKLV29-33_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1381					GRCh38	V40	FIP1L1_BGKLV29-33/Aligned.sortedByCoord.out.bam		ENCORE2	20542
FIP1L1_BGKLV29-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1381					GRCh38	V40	FIP1L1_BGKLV29-33/Aligned.sortedByCoord.out.bam		ENCORE2	20572
FIP1L1_BGKLV29-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1381					GRCh38	V40	FIP1L1_BGKLV29-33/Aligned.sortedByCoord.out.bam		ENCORE2	20602
FIP1L1_BGKLV29-33_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1381					GRCh38	V40	FIP1L1_BGKLV29-33_GTGGCC_L002_001.R1.fastq.gz,FIP1L1_BGKLV29-33_GTGGCC_L002_001.R2.fastq.gz		ENCORE2	20632
FIP1L1_BGKLV29-34_GTTTCG_L002_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1382	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20423
FIP1L1_BGKLV29-34_GTTTCG_L002_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1382	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20453
FIP1L1_BGKLV29-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1382					GRCh38	V40	FIP1L1_BGKLV29-34_GTTTCG_L002_001.R1.fastq.gz,FIP1L1_BGKLV29-34_GTTTCG_L002_001.R2.fastq.gz		ENCORE2	20483
FIP1L1_BGKLV29-34_Signal.Unique.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1382					GRCh38	V40	FIP1L1_BGKLV29-34/Aligned.sortedByCoord.out.bam		ENCORE2	20513
FIP1L1_BGKLV29-34_Signal.Unique.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1382					GRCh38	V40	FIP1L1_BGKLV29-34/Aligned.sortedByCoord.out.bam		ENCORE2	20543
FIP1L1_BGKLV29-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1382					GRCh38	V40	FIP1L1_BGKLV29-34/Aligned.sortedByCoord.out.bam		ENCORE2	20573
FIP1L1_BGKLV29-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1382					GRCh38	V40	FIP1L1_BGKLV29-34/Aligned.sortedByCoord.out.bam		ENCORE2	20603
FIP1L1_BGKLV29-34_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1382					GRCh38	V40	FIP1L1_BGKLV29-34_GTTTCG_L002_001.R1.fastq.gz,FIP1L1_BGKLV29-34_GTTTCG_L002_001.R2.fastq.gz		ENCORE2	20633