ABCF1 RNA-Seq in HepG2

General Information


RBP	ABCF1
Cell_Line	HepG2
Method	shRNA
Exp_Name	ABCF1-BGHLV30-HepG2
ENCODE_series_ID	ENCSR266ZIC
Batch_ID	BGHLV30
Pool ID	Pool-151215C
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR610VTA
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	ABCF1_BGHLV30-3
Rep2	ABCF1_BGHLV30-4
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	80.3
Rep2_WB	78.6
Antibody Cat#	A301-999A
Antibody Lot#	A301-999A
Antibody DCC ID	ENCAB710VED
Status	Released
Project	ENCODE3
ID	676

Experiment Information (Status: Released)

	BGHLV30-3	BGHLV30-4
idx	687	688
TRCN#_or_BGC#	TRCN0000157281	TRCN0000157281
shRNA_or_gRNA_sequence	GCGTCTTAAGAAGCTCTCAGT	GCGTCTTAAGAAGCTCTCAGT
PAM
Name	ABCF1	ABCF1
Sample_ID	BGHLV30-3	BGHLV30-4
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	ABCF1	ABCF1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	cgccaagccatgttagaaaa
RT-qPCR_primer-R	tctgcattgacgaacagctc
protein_conc	2992	2442
WB_result	80.3	78.6
Ave_WB	79.5
WB_DONE_date	9/18/2015
MW	96kDa
IP	1	1
antibody_Cat#	A301-999A	A301-999A
Antibody DCC ID	ENCAB710VED	ENCAB710VED
submitted_to_DCC_date	10/26/16
Rep1_TPM	44.8	0
Rep2_TPM	45.5	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2774	2775

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ABCF1	Product_ID: A301-999A Lot_ID: 1 Source: Bethyl Labs Target Name: ABCF1-human

Experiment Status

	BGHLV30-3	BGHLV30-4
Sample_ID	BGHLV30-3	BGHLV30-4
Sample Name	ABCF1_BGHLV30-3	ABCF1_BGHLV30-4
Sample Name	ABCF1_BGHLV30-3	ABCF1_BGHLV30-4
RBP	ABCF1	ABCF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1042	1043

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-3	BGHLV30-4
Sample #
Sample Name	ABCF1-BGHLV30-3	ABCF1-BGHLV30-4
Sample_Name_Alias	ABCF1_BGHLV30-3	ABCF1_BGHLV30-4
Index Well Position	S20	S21
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/C9.png	DNA_Library_LV28-29-30/set1/D9.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/C4.png	RNA_Library_LV29-30-31-32/set1/D4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-3	BGHLV30-4
RBP	ABCF1	ABCF1
Batch_ID	BGHLV30	BGHLV30
WB_result	80.300	78.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2734	2735

Sequencing Information

	BGHLV30-3	BGHLV30-4
Sample_ID	BGHLV30-3	BGHLV30-4
Sample Name	ABCF1_BGHLV30-3	ABCF1_BGHLV30-4
Pool ID	Pool-151215C	Pool-151215C
LocalServer_folder	set30	set30
total_reads	196,054,210	69,749,684
total_aligned_reads	164,436,614	56,934,958
unique_aligned_reads	153,875,678	53,455,030
percent_uniqueAligned	0.78486	0.76638
correlation_replicates	0.999068	0.999068
spikein_reads	541,946	183,812
percent_spikeins	0.00276	0.00264
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1360	1361

Data Submission Information

	BGHLV30-3	BGHLV30-3
ENCODE_alias	brenton-graveley:ABCF1_BGHLV30	brenton-graveley:ABCF1-BGHLV30-HepG2
ENCODE_accession	ENCSR610VTA	ENCSR266ZIC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-3	BGHLV30-3
Sample Name	ABCF1_BGHLV30-3	ABCF1_BGHLV30-3
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3070	6576

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
ABCF1_BGHLV30-3_GTGGCC_L008_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1360	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20698
ABCF1_BGHLV30-3_GTGGCC_L008_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1360	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20732
ABCF1_BGHLV30-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1360					GRCh38	V40	ABCF1_BGHLV30-3_GTGGCC_L008_001.R1.fastq.gz,ABCF1_BGHLV30-3_GTGGCC_L008_001.R2.fastq.gz		ENCORE2	20766
ABCF1_BGHLV30-3_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	1360					GRCh38	V40	ABCF1_BGHLV30-3/Aligned.sortedByCoord.out.bam		ENCORE2	20800
ABCF1_BGHLV30-3_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	1360					GRCh38	V40	ABCF1_BGHLV30-3/Aligned.sortedByCoord.out.bam		ENCORE2	20834
ABCF1_BGHLV30-3_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	1360					GRCh38	V40	ABCF1_BGHLV30-3/Aligned.sortedByCoord.out.bam		ENCORE2	20868
ABCF1_BGHLV30-3_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	1360					GRCh38	V40	ABCF1_BGHLV30-3/Aligned.sortedByCoord.out.bam		ENCORE2	20902
ABCF1_BGHLV30-3_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1360					GRCh38	V40	ABCF1_BGHLV30-3_GTGGCC_L008_001.R1.fastq.gz,ABCF1_BGHLV30-3_GTGGCC_L008_001.R2.fastq.gz		ENCORE2	20936
ABCF1_BGHLV30-4_GTTTCG_L008_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1361	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20699
ABCF1_BGHLV30-4_GTTTCG_L008_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1361	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20733
ABCF1_BGHLV30-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1361					GRCh38	V40	ABCF1_BGHLV30-4_GTTTCG_L008_001.R1.fastq.gz,ABCF1_BGHLV30-4_GTTTCG_L008_001.R2.fastq.gz		ENCORE2	20767
ABCF1_BGHLV30-4_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	1361					GRCh38	V40	ABCF1_BGHLV30-4/Aligned.sortedByCoord.out.bam		ENCORE2	20801
ABCF1_BGHLV30-4_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	1361					GRCh38	V40	ABCF1_BGHLV30-4/Aligned.sortedByCoord.out.bam		ENCORE2	20835
ABCF1_BGHLV30-4_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	1361					GRCh38	V40	ABCF1_BGHLV30-4/Aligned.sortedByCoord.out.bam		ENCORE2	20869
ABCF1_BGHLV30-4_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	1361					GRCh38	V40	ABCF1_BGHLV30-4/Aligned.sortedByCoord.out.bam		ENCORE2	20903
ABCF1_BGHLV30-4_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1361					GRCh38	V40	ABCF1_BGHLV30-4_GTTTCG_L008_001.R1.fastq.gz,ABCF1_BGHLV30-4_GTTTCG_L008_001.R2.fastq.gz		ENCORE2	20937