FKBP4 RNA-Seq in HepG2

General Information


RBP	FKBP4
Cell_Line	HepG2
Method	shRNA
Exp_Name	FKBP4-BGHLV17-HepG2
ENCODE_series_ID	ENCSR018EQF
Batch_ID	BGHLV17
Pool ID	Pool-141001
Local_Set_Name	set17
ENCODE_KD_Exp_ID	ENCSR639LKS
ENCODE_CN_Exp_ID	ENCSR856ZRV
Rep1	FKBP4_BGHLV17_15
Rep2	FKBP4_BGHLV17_16
CN1	NT_BGHLV17_63
CN2	NT_BGHLV17_64
Rep1_qPCR	64.5
Rep2_qPCR	71.8
Rep1_WB	52.8
Rep2_WB	60.5
Antibody Cat#	A301-427A
Antibody Lot#	A301-427A
Antibody DCC ID	ENCAB145YUK
Status	Released
Project	ENCODE3
ID	433

Experiment Information (Status: Released)

	BGHLV17-15	BGHLV17-16
idx	251	252
TRCN#_or_BGC#	TRCN0000157250	TRCN0000157250
shRNA_or_gRNA_sequence	GAAGGCTATGCTAAGCCCAAT	GAAGGCTATGCTAAGCCCAAT
PAM
Name	FKBP4	FKBP4
Sample_ID	BGHLV17-15	BGHLV17-16
transduction_Date	8/19/2014	8/19/2014
days
RBP_name	FKBP4	FKBP4
qPCR_result	64.5	71.8
Ave_qPCR	68.1
RT-qPCR_primer-F	ctgacggaagaggaagatgg
RT-qPCR_primer-R	agtgcaacctccacgatagc
protein_conc	3128	2950
WB_result	52.8	60.5
Ave_WB	56.6
WB_DONE_date	3/19/2015
MW	59kDa
IP	1	1
antibody_Cat#	A301-427A	A301-427A
Antibody DCC ID	ENCAB145YUK	ENCAB145YUK
submitted_to_DCC_date	4/2/2015
Rep1_TPM	45.7	0
Rep2_TPM	63.1	0
Action
Library_start_date	9/26/2014	9/26/2014
repeat_library
Note
ID	2316	2317

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FKBP4	Product_ID: A301-427A Lot_ID: 1 Source: Bethyl Labs Target Name: FKBP4-human

Experiment Status

	BGHLV17-15	BGHLV17-16
Sample_ID	BGHLV17-15	BGHLV17-16
Sample Name	FKBP4_BGHLV17_15	FKBP4_BGHLV17_16
Sample Name	FKBP4_BGHLV17_15	FKBP4_BGHLV17_16
RBP	FKBP4	FKBP4
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	592	593

Library-Prep
Sequencing

Library-Prep Information

	BGHLV17-15	BGHLV17-16
Sample #
Sample Name	FKBP4-BGHLV17-15	FKBP4-BGHLV17-16
Sample_Name_Alias	FKBP4_BGHLV17_15	FKBP4_BGHLV17_16
Index Well Position	S09	S10
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-26	2014-09-26
Lib_ID	Lib-140926	Lib-140926
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/A2.png	DNA_Library_LV16-17/set1/B2.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/A4.png	RNA_Library_LV16-17-18/set1/B4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV17-15	BGHLV17-16
RBP	FKBP4	FKBP4
Batch_ID	BGHLV17	BGHLV17
WB_result	52.800	60.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2276	2277

Sequencing Information

	BGHLV17-15	BGHLV17-16
Sample_ID	BGHLV17-15	BGHLV17-16
Sample Name	FKBP4_BGHLV17_15	FKBP4_BGHLV17_16
Pool ID	Pool-141001	Pool-141001
LocalServer_folder	set17	set17
total_reads	34,710,000	68,830,000
total_aligned_reads	30,914,586	61,493,660
unique_aligned_reads	29,294,848	58,280,990
percent_uniqueAligned	0.84399	0.84674
correlation_replicates	0.994483	0.994483
spikein_reads	153,474	142,080
percent_spikeins	0.00442	0.00206
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	918	919

Data Submission Information

	BGHLV17-15	BGHLV17-15
ENCODE_alias	brenton-graveley:FKBP4_BGHLV17	brenton-graveley:FKBP4-BGHLV17-HepG2
ENCODE_accession	ENCSR639LKS	ENCSR018EQF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV17-15	BGHLV17-15
Sample Name	FKBP4_BGHLV17_15	FKBP4_BGHLV17_15
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2864	6713

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
FKBP4_BGHLV17_15_GATCAG_L002_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	918	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14500
FKBP4_BGHLV17_15_GATCAG_L002_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	918	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14538
FKBP4_BGHLV17_15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	918					GRCh38	V40	FKBP4_BGHLV17_15_GATCAG_L002_R1_001.fastq.gz,FKBP4_BGHLV17_15_GATCAG_L002_R2_001.fastq.gz		ENCORE2	14576
FKBP4_BGHLV17_15_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	918					GRCh38	V40	FKBP4_BGHLV17_15/Aligned.sortedByCoord.out.bam		ENCORE2	14614
FKBP4_BGHLV17_15_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	918					GRCh38	V40	FKBP4_BGHLV17_15/Aligned.sortedByCoord.out.bam		ENCORE2	14652
FKBP4_BGHLV17_15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	918					GRCh38	V40	FKBP4_BGHLV17_15/Aligned.sortedByCoord.out.bam		ENCORE2	14690
FKBP4_BGHLV17_15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	918					GRCh38	V40	FKBP4_BGHLV17_15/Aligned.sortedByCoord.out.bam		ENCORE2	14728
FKBP4_BGHLV17_15_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	918					GRCh38	V40	FKBP4_BGHLV17_15_GATCAG_L002_R1_001.fastq.gz,FKBP4_BGHLV17_15_GATCAG_L002_R2_001.fastq.gz		ENCORE2	14766
FKBP4_BGHLV17_16_TAGCTT_L002_R1_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	919	HiSeq2000	100	paired-ended	1				NT_BGHLV17_63_ATCACG_L001_R1_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R1_001.fastq.gz	ENCODE3	14501
FKBP4_BGHLV17_16_TAGCTT_L002_R2_001.fastq.gz	ENCODE_DATA/set17/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	919	HiSeq2000	100	paired-ended	2				NT_BGHLV17_63_ATCACG_L001_R2_001.merged.fastq.gz,NT_BGHLV17_64_CGATGT_L001_R2_001.fastq.gz	ENCODE3	14539
FKBP4_BGHLV17_16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	919					GRCh38	V40	FKBP4_BGHLV17_16_TAGCTT_L002_R1_001.fastq.gz,FKBP4_BGHLV17_16_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	14577
FKBP4_BGHLV17_16_Signal.Unique.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	919					GRCh38	V40	FKBP4_BGHLV17_16/Aligned.sortedByCoord.out.bam		ENCORE2	14615
FKBP4_BGHLV17_16_Signal.Unique.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	919					GRCh38	V40	FKBP4_BGHLV17_16/Aligned.sortedByCoord.out.bam		ENCORE2	14653
FKBP4_BGHLV17_16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	919					GRCh38	V40	FKBP4_BGHLV17_16/Aligned.sortedByCoord.out.bam		ENCORE2	14691
FKBP4_BGHLV17_16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set17/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	919					GRCh38	V40	FKBP4_BGHLV17_16/Aligned.sortedByCoord.out.bam		ENCORE2	14729
FKBP4_BGHLV17_16_quant.sf	ENCODE_DATA/set17/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	919					GRCh38	V40	FKBP4_BGHLV17_16_TAGCTT_L002_R1_001.fastq.gz,FKBP4_BGHLV17_16_TAGCTT_L002_R2_001.fastq.gz		ENCORE2	14767