FASTKD2 RNA-Seq in HepG2

General Information


RBP	FASTKD2
Cell_Line	HepG2
Method	shRNA
Exp_Name	FASTKD2-BGHLV14-HepG2
ENCODE_series_ID	ENCSR384FLZ
Batch_ID	BGHLV14
Pool ID	Pool-140915
Local_Set_Name	set14
ENCODE_KD_Exp_ID	ENCSR716WZH
ENCODE_CN_Exp_ID	ENCSR003EKR
Rep1	FASTKD2_BGHLV14-19
Rep2	FASTKD2_BGHLV14-20
CN1	NT_BGHLV14-1_1
CN2	NT_BGHLV14-2_1
Rep1_qPCR	60.3
Rep2_qPCR	50.2
Rep1_WB	31.5
Rep2_WB	31.7
Antibody Cat#	A303-788A
Antibody Lot#	A303-788A
Antibody DCC ID	ENCAB541LFT
Status	Released
Project	ENCODE3
ID	392

Experiment Information (Status: Released)

	BGHLV14-19	BGHLV14-20
idx	115	116
TRCN#_or_BGC#	TRCN0000145126	TRCN0000145126
shRNA_or_gRNA_sequence	GCTTTCAAACAAAGGGCATAA	GCTTTCAAACAAAGGGCATAA
PAM
Name	FASTKD2	FASTKD2
Sample_ID	BGHLV14-19	BGHLV14-20
transduction_Date	7/4/2014	7/4/2014
days
RBP_name	FASTKD2	FASTKD2
qPCR_result	60.3	50.2
Ave_qPCR	55.3
RT-qPCR_primer-F	GCATTTGAATGCAATGGGT
RT-qPCR_primer-R	TGTGACTGCATCTTCCATCTCT
protein_conc	4751	4408
WB_result	31.5	31.7
Ave_WB	31.6
WB_DONE_date	4/14/2015
MW
IP	1MW	1MW
antibody_Cat#	A303-788A	A303-788A
Antibody DCC ID	ENCAB541LFT	ENCAB541LFT
submitted_to_DCC_date	5/4/2015
Rep1_TPM	16.5	0
Rep2_TPM	13	0
Action
Library_start_date	7/30/2014	7/30/2014
repeat_library
Note
ID	2172	2173

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FASTKD2	Product_ID: A303-788A Lot_ID: 1 Source: Bethyl Labs Target Name: FASTKD2-human

Experiment Status

	BGHLV14-19	BGHLV14-20
Sample_ID	BGHLV14-19	BGHLV14-20
Sample Name	FASTKD2_BGHLV14-19	FASTKD2_BGHLV14-20
Sample Name	FASTKD2_BGHLV14-19	FASTKD2_BGHLV14-20
RBP	FASTKD2	FASTKD2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-11-04	2014-11-04
Project	ENCODE3	ENCODE3
Note
ID	506	507

Library-Prep
Sequencing

Library-Prep Information

	BGHLV14-19	BGHLV14-20
Sample #
Sample Name	FASTKD2-BGHLV14-19	FASTKD2-BGHLV14-20
Sample_Name_Alias	FASTKD2_BGHLV14-19	FASTKD2_BGHLV14-20
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-07-30	2014-07-30
Lib_ID	Lib-140730	Lib-140730
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV13-14/set1/H9.png	DNA_Library_LV13-14/set1/A10.png
RIN	9.4	9.6
libSample_RNA_Well	RNA_Library_LV13-14-16/set1/C6.png	RNA_Library_LV13-14-16/set1/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV14-19	BGHLV14-20
RBP	FASTKD2	FASTKD2
Batch_ID	BGHLV14	BGHLV14
WB_result	31.500	31.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2190	2191

Sequencing Information

	BGHLV14-19	BGHLV14-20
Sample_ID	BGHLV14-19	BGHLV14-20
Sample Name	FASTKD2_BGHLV14-19	FASTKD2_BGHLV14-20
Pool ID	Pool-140915	Pool-140915
LocalServer_folder	set14	set14
total_reads	53,890,000	48,480,000
total_aligned_reads	50,981,478	45,640,744
unique_aligned_reads	48,050,148	43,058,420
percent_uniqueAligned	0.89163	0.88817
correlation_replicates	0.997840	0.997840
spikein_reads	239,908	186,678
percent_spikeins	0.00445	0.00385
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	832	833

Data Submission Information

	BGHLV14-19	BGHLV14-19
ENCODE_alias	brenton-graveley:FASTKD2_BGHLV14	brenton-graveley:FASTKD2-BGHLV14-HepG2
ENCODE_accession	ENCSR716WZH	ENCSR384FLZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV14-19	BGHLV14-19
Sample Name	FASTKD2_BGHLV14-19	FASTKD2_BGHLV14-19
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-10-30	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2803	6709

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
FASTKD2_BGHLV14-19_ACTGAT_L002_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	832	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13798
FASTKD2_BGHLV14-19_ACTGAT_L002_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	832	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13860
FASTKD2_BGHLV14-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	832					GRCh38	V40	FASTKD2_BGHLV14-19_ACTGAT_L002_R1_001.fastq.gz,FASTKD2_BGHLV14-19_ACTGAT_L002_R2_001.fastq.gz		ENCORE2	13922
FASTKD2_BGHLV14-19_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	832					GRCh38	V40	FASTKD2_BGHLV14-19/Aligned.sortedByCoord.out.bam		ENCORE2	13984
FASTKD2_BGHLV14-19_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	832					GRCh38	V40	FASTKD2_BGHLV14-19/Aligned.sortedByCoord.out.bam		ENCORE2	14046
FASTKD2_BGHLV14-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	832					GRCh38	V40	FASTKD2_BGHLV14-19/Aligned.sortedByCoord.out.bam		ENCORE2	14108
FASTKD2_BGHLV14-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	832					GRCh38	V40	FASTKD2_BGHLV14-19/Aligned.sortedByCoord.out.bam		ENCORE2	14170
FASTKD2_BGHLV14-19_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	832					GRCh38	V40	FASTKD2_BGHLV14-19_ACTGAT_L002_R1_001.fastq.gz,FASTKD2_BGHLV14-19_ACTGAT_L002_R2_001.fastq.gz		ENCORE2	14232
FASTKD2_BGHLV14-20_ATTCCT_L002_R1_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	833	HiSeq2000	100	paired-ended	1				NT_BGHLV14-1_1_ACAGTG_L008_R1_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R1_001.fastq.gz	ENCODE3	13799
FASTKD2_BGHLV14-20_ATTCCT_L002_R2_001.fastq.gz	ENCODE_DATA/set14/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	833	HiSeq2000	100	paired-ended	2				NT_BGHLV14-1_1_ACAGTG_L008_R2_001.fastq.gz,NT_BGHLV14-2_1_GCCAAT_L008_R2_001.fastq.gz	ENCODE3	13861
FASTKD2_BGHLV14-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	833					GRCh38	V40	FASTKD2_BGHLV14-20_ATTCCT_L002_R1_001.fastq.gz,FASTKD2_BGHLV14-20_ATTCCT_L002_R2_001.fastq.gz		ENCORE2	13923
FASTKD2_BGHLV14-20_Signal.Unique.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	833					GRCh38	V40	FASTKD2_BGHLV14-20/Aligned.sortedByCoord.out.bam		ENCORE2	13985
FASTKD2_BGHLV14-20_Signal.Unique.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	833					GRCh38	V40	FASTKD2_BGHLV14-20/Aligned.sortedByCoord.out.bam		ENCORE2	14047
FASTKD2_BGHLV14-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	833					GRCh38	V40	FASTKD2_BGHLV14-20/Aligned.sortedByCoord.out.bam		ENCORE2	14109
FASTKD2_BGHLV14-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set14/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	833					GRCh38	V40	FASTKD2_BGHLV14-20/Aligned.sortedByCoord.out.bam		ENCORE2	14171
FASTKD2_BGHLV14-20_quant.sf	ENCODE_DATA/set14/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	833					GRCh38	V40	FASTKD2_BGHLV14-20_ATTCCT_L002_R1_001.fastq.gz,FASTKD2_BGHLV14-20_ATTCCT_L002_R2_001.fastq.gz		ENCORE2	14233