ABCF1 RNA-Seq in K562

General Information


RBP	ABCF1
Cell_Line	K562
Method	shRNA
Exp_Name	ABCF1-BGKLV29-K562
ENCODE_series_ID	ENCSR242RKD
Batch_ID	BGKLV29
Pool ID	Pool-151215C
Local_Set_Name	set29
ENCODE_KD_Exp_ID	ENCSR721MXZ
ENCODE_CN_Exp_ID	ENCSR032YMP
Rep1	ABCF1_BGKLV29-3
Rep2	ABCF1_BGKLV29-4
CN1	NT_BGKLV29-1
CN2	NT_BGKLV29-2
Rep1_qPCR	67.5
Rep2_qPCR	58.0
Rep1_WB	69.0
Rep2_WB	69.7
Antibody Cat#	A301-999A
Antibody Lot#	A301-999A
Antibody DCC ID	ENCAB710VED
Status	Released
Project	ENCODE3
ID	663

Experiment Information (Status: Released)

	BGKLV29-3	BGKLV29-4
idx	536	537
TRCN#_or_BGC#	TRCN0000157281	TRCN0000157281
shRNA_or_gRNA_sequence	GCGTCTTAAGAAGCTCTCAGT	GCGTCTTAAGAAGCTCTCAGT
PAM
Name	ABCF1	ABCF1
Sample_ID	BGKLV29-3	BGKLV29-4
transduction_Date	8/11/2015	8/11/2015
days
RBP_name	ABCF1	ABCF1
qPCR_result	67.5	58.0
Ave_qPCR	62.8
RT-qPCR_primer-F	cgccaagccatgttagaaaa
RT-qPCR_primer-R	tctgcattgacgaacagctc
protein_conc	3181	3133
WB_result	69.0	69.7
Ave_WB	69.3
WB_DONE_date	3/16/2016
MW	96kDa	WES
IP	1	1
antibody_Cat#	A301-999A	A301-999A
Antibody DCC ID	ENCAB710VED	ENCAB710VED
submitted_to_DCC_date	3/18/2016
Rep1_TPM	111.491004	0
Rep2_TPM	64.4324395	0
Action
Library_start_date	11/2/2015	11/2/2015
repeat_library
Note	x	x
ID	615	616

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

	BGKLV29-3	BGKLV29-4
Sample_ID	BGKLV29-3	BGKLV29-4
Sample Name	ABCF1_BGKLV29-3	ABCF1_BGKLV29-4
Sample Name	ABCF1_BGKLV29-3	ABCF1_BGKLV29-4
RBP	ABCF1	ABCF1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	1012	1013

Library-Prep
Sequencing

Library-Prep Information

	BGKLV29-3	BGKLV29-4
Sample #
Sample Name	ABCF1-BGKLV29-3	ABCF1-BGKLV29-4
Sample_Name_Alias	ABCF1_BGKLV29-3	ABCF1_BGKLV29-4
Index Well Position	S11	S12
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/C5.png	DNA_Library_LV28-29-30/set1/D5.png
RIN	9.9	9.6
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/G10.png	RNA_Library_LV26-27-28-29/set1/H10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV29-3	BGKLV29-4
RBP	ABCF1	ABCF1
Batch_ID	BGKLV29	BGKLV29
WB_result	69.000	69.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2704	2705

Sequencing Information

	BGKLV29-3	BGKLV29-4
Sample_ID	BGKLV29-3	BGKLV29-4
Sample Name	ABCF1_BGKLV29-3	ABCF1_BGKLV29-4
Pool ID	Pool-151215C	Pool-151215C
LocalServer_folder	set29	set29
total_reads	119,922,306	121,948,720
total_aligned_reads	91,489,914	97,312,470
unique_aligned_reads	82,878,090	88,176,314
percent_uniqueAligned	0.69110	0.72306
correlation_replicates	0.998673	0.998673
spikein_reads	461,452	507,346
percent_spikeins	0.00385	0.00416
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1346	1347

Data Submission Information

	BGKLV29-3	BGKLV29-3
ENCODE_alias	brenton-graveley:ABCF1_BGKLV29	brenton-graveley:ABCF1-BGKLV29-K562
ENCODE_accession	ENCSR721MXZ	ENCSR242RKD
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV29-3	BGKLV29-3
Sample Name	ABCF1_BGKLV29-3	ABCF1_BGKLV29-3
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3055	6577

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_BGKLV29-3_GGCTAC_L005_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1346	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20414
ABCF1_BGKLV29-3_GGCTAC_L005_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1346	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20444
ABCF1_BGKLV29-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1346					GRCh38	V40	ABCF1_BGKLV29-3_GGCTAC_L005_001.R1.fastq.gz,ABCF1_BGKLV29-3_GGCTAC_L005_001.R2.fastq.gz		ENCORE2	20474
ABCF1_BGKLV29-3_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	1346					GRCh38	V40	ABCF1_BGKLV29-3/Aligned.sortedByCoord.out.bam		ENCORE2	20504
ABCF1_BGKLV29-3_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	1346					GRCh38	V40	ABCF1_BGKLV29-3/Aligned.sortedByCoord.out.bam		ENCORE2	20534
ABCF1_BGKLV29-3_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	1346					GRCh38	V40	ABCF1_BGKLV29-3/Aligned.sortedByCoord.out.bam		ENCORE2	20564
ABCF1_BGKLV29-3_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	1346					GRCh38	V40	ABCF1_BGKLV29-3/Aligned.sortedByCoord.out.bam		ENCORE2	20594
ABCF1_BGKLV29-3_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1346					GRCh38	V40	ABCF1_BGKLV29-3_GGCTAC_L005_001.R1.fastq.gz,ABCF1_BGKLV29-3_GGCTAC_L005_001.R2.fastq.gz		ENCORE2	20624
ABCF1_BGKLV29-4_CTTGTA_L005_001.R1.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1347	HiSeq2500	100	paired-ended	1				NT_BGKLV29-1_GATCAG_L005_001.R1.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R1.fastq.gz	ENCODE3	20415
ABCF1_BGKLV29-4_CTTGTA_L005_001.R2.fastq.gz	ENCODE_DATA/set29/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1347	HiSeq2500	100	paired-ended	2				NT_BGKLV29-1_GATCAG_L005_001.R2.fastq.gz,NT_BGKLV29-2_TAGCTT_L005_001.R2.fastq.gz	ENCODE3	20445
ABCF1_BGKLV29-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set29/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1347					GRCh38	V40	ABCF1_BGKLV29-4_CTTGTA_L005_001.R1.fastq.gz,ABCF1_BGKLV29-4_CTTGTA_L005_001.R2.fastq.gz		ENCORE2	20475
ABCF1_BGKLV29-4_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	1347					GRCh38	V40	ABCF1_BGKLV29-4/Aligned.sortedByCoord.out.bam		ENCORE2	20505
ABCF1_BGKLV29-4_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	1347					GRCh38	V40	ABCF1_BGKLV29-4/Aligned.sortedByCoord.out.bam		ENCORE2	20535
ABCF1_BGKLV29-4_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	1347					GRCh38	V40	ABCF1_BGKLV29-4/Aligned.sortedByCoord.out.bam		ENCORE2	20565
ABCF1_BGKLV29-4_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	1347					GRCh38	V40	ABCF1_BGKLV29-4/Aligned.sortedByCoord.out.bam		ENCORE2	20595
ABCF1_BGKLV29-4_quant.sf	ENCODE_DATA/set29/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1347					GRCh38	V40	ABCF1_BGKLV29-4_CTTGTA_L005_001.R1.fastq.gz,ABCF1_BGKLV29-4_CTTGTA_L005_001.R2.fastq.gz		ENCORE2	20625