ABT1 RNA-Seq in HepG2

General Information


RBP	ABT1
Cell_Line	HepG2
Method	shRNA
Exp_Name	ABT1-BGHLV37-HepG2
ENCODE_series_ID	ENCSR456IPG
Batch_ID	BGHLV37
Pool ID	Pool-180316
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR756VLW
ENCODE_CN_Exp_ID	ENCSR225PRV
Rep1	ABT1-BGHLV37-3C
Rep2	ABT1-BGHLV37-4C
CN1	non-target-BGHLV37-1C
CN2	non-target-BGHLV37-2C
Rep1_qPCR	72.6
Rep2_qPCR	87.3
Rep1_WB	78.7
Rep2_WB	79.7
Antibody Cat#	A304-044A
Antibody Lot#	A304-044A
Antibody DCC ID	ENCAB891MJI
Status	Released
Project	ENCODE4
ID	261

Experiment Information (Status: Released)

	BGHLV37-3	BGHLV37-4
idx	915	916
TRCN#_or_BGC#	TRCN0000017607	TRCN0000017607
shRNA_or_gRNA_sequence	CCGGTTCGTGAGACGCAAGAA	CCGGTTCGTGAGACGCAAGAA
PAM
Name	ABT1	ABT1
Sample_ID	BGHLV37-3	BGHLV37-4
transduction_Date	9/1/16	9/1/16
days
RBP_name	ABT1	ABT1
qPCR_result	72.6	87.3
Ave_qPCR	79.9
RT-qPCR_primer-F	cgtcttctttcaggctgagg
RT-qPCR_primer-R	ttggtgtaggaccgcttttt
protein_conc	3552	3275
WB_result	78.7	79.7
Ave_WB	79.2
WB_DONE_date	9/14/16
MW	31kDa
IP	1	1
antibody_Cat#	A304-044A	A304-044A
Antibody DCC ID	ENCAB891MJI	ENCAB891MJI
submitted_to_DCC_date	10/26/16
Rep1_TPM	8.5	0
Rep2_TPM	7.6	0
Action
Library_start_date	12/18/17	12/18/17
repeat_library
Note
ID	3008	3009

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ABT1	Product_ID: A304-044A Lot_ID: 1 Source: Bethyl Labs Target Name: ABT1-human

Experiment Status

	BGHLV37-3	BGHLV37-4
Sample_ID	BGHLV37-3	BGHLV37-4
Sample Name
Sample Name	ABT1-BGHLV37-3C	ABT1-BGHLV37-4C
RBP	ABT1	ABT1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6433	6434

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-3	BGHLV37-4
Sample #	17	18
Sample Name	ABT1-BGHLV37-3C	ABT1-BGHLV37-4C
Sample_Name_Alias
Index Well Position	S03	S04
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2018-01-02	2018-01-02
Lib_ID	Lib-180102	Lib-180102
Tecan_Location
Tecan
Tecan_date
Size_bp	309	313
Peak_Molarity	28.20	24.30
libSampleQC_DNA_Well	DNA_Library_set40/set1/C5.png	DNA_Library_set40/set1/D5.png
RIN	9.2	9.3
libSample_RNA_Well	RNA_Library_set40/set1/A1.png	RNA_Library_set40/set1/B1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHLV37-3	BGHLV37-4
RBP	ABT1	ABT1
Batch_ID	BGHLV37	BGHLV37
WB_result	78.700	79.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	940	941

Sequencing Information

	BGHLV37-3	BGHLV37-3	BGHLV37-4	BGHLV37-4
Sample_ID	BGHLV37-3	BGHLV37-3	BGHLV37-4	BGHLV37-4
Sample Name	ABT1-BGHLV37-3C	ABT1-BGHLV37-3C	ABT1-BGHLV37-4C	ABT1-BGHLV37-4C
Pool ID	Pool-180109	Pool-180316	Pool-180109	Pool-180316
LocalServer_folder	set40_H	set40_H	set40_H	set40_H
total_reads	18,961,208	34,975,438	18,919,764	38,607,708
total_aligned_reads	16,185,106	30,282,164	15,993,702	33,337,574
unique_aligned_reads	15,237,788	28,512,930	15,054,920	31,376,096
percent_uniqueAligned	0.80363	0.81523	0.79572	0.81269
correlation_replicates	0.999085		0.999085
spikein_reads	6,186	11,572	9,636	20,076
percent_spikeins	0.00033	0.00033	0.00051	0.00052
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	343	399	344	400

Data Submission Information

	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-4	BGHLV37-4	BGHLV37-4	BGHLV37-4	BGHLV37-4	BGHLV37-4
ENCODE_alias	brenton-graveley:ABT1-BGHLV37-C	brenton-graveley:ABT1-BGHLV37-3C	brenton-graveley:L-ABT1-BGHLV37-3C	brenton-graveley:ABT1-BGHLV37-3C_TTAGGC_ACBYWVANXX_L001_001.R1.fastq.gz	brenton-graveley:ABT1-BGHLV37-3C_TTAGGC_AHFKCFBCX2_L001_001.R1.fastq.gz	brenton-graveley:ABT1-BGHLV37-3C_TTAGGC_ACBYWVANXX_L001_001.R2.fastq.gz	brenton-graveley:ABT1-BGHLV37-3C_TTAGGC_AHFKCFBCX2_L001_001.R2.fastq.gz	brenton-graveley:ABT1-BGHLV37-HepG2	brenton-graveley:ABT1-BGHLV37-4C	brenton-graveley:L-ABT1-BGHLV37-4C	brenton-graveley:ABT1-BGHLV37-4C_TGACCA_ACBYWVANXX_L001_001.R1.fastq.gz	brenton-graveley:ABT1-BGHLV37-4C_TGACCA_AHFKCFBCX2_L001_001.R1.fastq.gz	brenton-graveley:ABT1-BGHLV37-4C_TGACCA_ACBYWVANXX_L001_001.R2.fastq.gz	brenton-graveley:ABT1-BGHLV37-4C_TGACCA_AHFKCFBCX2_L001_001.R2.fastq.gz
ENCODE_accession	ENCSR756VLW	ENCBS561WGB	ENCLB790TRW	ENCFF031KRB	ENCFF876FSQ	ENCFF101MKM	ENCFF059XLR	ENCSR456IPG	ENCBS157VRK	ENCLB858UHU	ENCFF403NYJ	ENCFF517LKM	ENCFF846EMV	ENCFF765YYE
object_type	experiment	biosample	library	file_fastq1	file_fastq1	file_fastq2	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq1	file_fastq2	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-3	BGHLV37-4	BGHLV37-4	BGHLV37-4	BGHLV37-4	BGHLV37-4	BGHLV37-4
Sample Name	ABT1-BGHLV37-3C	ABT1-BGHLV37-3C	ABT1-BGHLV37-3C	ABT1-BGHLV37-3C	ABT1-BGHLV37-3C	ABT1-BGHLV37-3C	ABT1-BGHLV37-3C	ABT1-BGHLV37-3C	ABT1-BGHLV37-4C	ABT1-BGHLV37-4C	ABT1-BGHLV37-4C	ABT1-BGHLV37-4C	ABT1-BGHLV37-4C	ABT1-BGHLV37-4C
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol						LV40_biosample_protocol	LV40_library_protocol
protocol_URL		ABT1-BGHLV37-3C.pdf	L-ABT1-BGHLV37-3C.pdf						ABT1-BGHLV37-4C.pdf	L-ABT1-BGHLV37-4C.pdf
ID	1430	1458	1514	1570	1571	1607	1608	7058	1459	1515	1572	1573	1609	1610

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
ABT1-BGHLV37-3C_L001_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	343	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	23230
ABT1-BGHLV37-3C_L001_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	343	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	23238
ABT1-BGHLV37-3C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	343					GRCh38	V40	ABT1-BGHLV37-3C_L001_001.R1.fastq.gz,ABT1-BGHLV37-3C_L001_001.R2.fastq.gz		ENCORE2	23246
ABT1-BGHLV37-3C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	343					GRCh38	V40	ABT1-BGHLV37-3C/Aligned.sortedByCoord.out.bam		ENCORE2	23280
ABT1-BGHLV37-3C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	343					GRCh38	V40	ABT1-BGHLV37-3C/Aligned.sortedByCoord.out.bam		ENCORE2	23314
ABT1-BGHLV37-3C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	343					GRCh38	V40	ABT1-BGHLV37-3C/Aligned.sortedByCoord.out.bam		ENCORE2	23348
ABT1-BGHLV37-3C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	343					GRCh38	V40	ABT1-BGHLV37-3C/Aligned.sortedByCoord.out.bam		ENCORE2	23382
ABT1-BGHLV37-3C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	343					GRCh38	V40	ABT1-BGHLV37-3C_L001_001.R1.fastq.gz,ABT1-BGHLV37-3C_L001_001.R2.fastq.gz		ENCORE2	23416
ABT1-BGHLV37-4C_L001_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	344	HiSeq2500	100	paired-ended	1				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R1.fastq.gz,non-target-BGHLV37-2C_L001_001.R1.fastq.gz	ENCODE4	23231
ABT1-BGHLV37-4C_L001_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	344	HiSeq2500	100	paired-ended	2				non-target-BGHLV37-1C_ATCACG_ACBYWVANXX_L001_001.R2.fastq.gz,non-target-BGHLV37-2C_L001_001.R2.fastq.gz	ENCODE4	23239
ABT1-BGHLV37-4C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	344					GRCh38	V40	ABT1-BGHLV37-4C_L001_001.R1.fastq.gz,ABT1-BGHLV37-4C_L001_001.R2.fastq.gz		ENCORE2	23247
ABT1-BGHLV37-4C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	344					GRCh38	V40	ABT1-BGHLV37-4C/Aligned.sortedByCoord.out.bam		ENCORE2	23281
ABT1-BGHLV37-4C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	344					GRCh38	V40	ABT1-BGHLV37-4C/Aligned.sortedByCoord.out.bam		ENCORE2	23315
ABT1-BGHLV37-4C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	344					GRCh38	V40	ABT1-BGHLV37-4C/Aligned.sortedByCoord.out.bam		ENCORE2	23349
ABT1-BGHLV37-4C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	344					GRCh38	V40	ABT1-BGHLV37-4C/Aligned.sortedByCoord.out.bam		ENCORE2	23383
ABT1-BGHLV37-4C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	344					GRCh38	V40	ABT1-BGHLV37-4C_L001_001.R1.fastq.gz,ABT1-BGHLV37-4C_L001_001.R2.fastq.gz		ENCORE2	23417