XRN1 RNA-Seq in HepG2

General Information


RBP	XRN1
Cell_Line	HepG2
Method	shRNA
Exp_Name	XRN1-BGHLV37-HepG2
ENCODE_series_ID	ENCSR786TDX
Batch_ID	BGHLV37
Pool ID	Pool-180109
Local_Set_Name	set40_H
ENCODE_KD_Exp_ID	ENCSR676SDU
ENCODE_CN_Exp_ID	ENCSR225PRV
Rep1	XRN1-BGHLV37-99C
Rep2	XRN1-BGHLV37-100C
CN1	non-target-BGHLV37-1C
CN2	non-target-BGHLV37-2C
Rep1_qPCR	15.8
Rep2_qPCR	12.5
Rep1_WB	79.8
Rep2_WB	85.7
Antibody Cat#	A300-443A
Antibody Lot#	A300-443A
Antibody DCC ID	ENCAB231MQI
Status	Released
Project	ENCODE4
ID	267

Experiment Information (Status: Released)

	BGHLV37-99	BGHLV37-100
idx	1011	1012
TRCN#_or_BGC#	TRCN0000049674	TRCN0000049674
shRNA_or_gRNA_sequence	GCTGGTATTATCCTTATCATT	GCTGGTATTATCCTTATCATT
PAM
Name	XRN1	XRN1
Sample_ID	BGHLV37-99	BGHLV37-100
transduction_Date	9/1/16	9/1/16
days
RBP_name	XRN1	XRN1
qPCR_result	15.8	12.5
Ave_qPCR	14.1
RT-qPCR_primer-F	ggtgaaagagcatcagattcc
RT-qPCR_primer-R	tcattaggatgggagcactg
protein_conc	4371	3678
WB_result	79.8	85.7
Ave_WB	82.7
WB_DONE_date	10/18/16	wes
MW	194kDa
IP	1	1
antibody_Cat#	A300-443A	A300-443A
Antibody DCC ID	ENCAB231MQI	ENCAB231MQI
submitted_to_DCC_date	10/27/16
Rep1_TPM	4.2	0
Rep2_TPM	3.6	0
Action
Library_start_date	12/18/17	12/18/17
repeat_library
Note
ID	3104	3105

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
XRN1	Product_ID: A300-443A Lot_ID: 3 Source: Bethyl Labs Target Name: XRN1-human

Experiment Status

	BGHLV37-99	BGHLV37-100
Sample_ID	BGHLV37-99	BGHLV37-100
Sample Name
Sample Name	XRN1-BGHLV37-99C	XRN1-BGHLV37-100C
RBP	XRN1	XRN1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6445	6446

Library-Prep
Sequencing

Library-Prep Information

	BGHLV37-99	BGHLV37-100
Sample #	29	30
Sample Name	XRN1-BGHLV37-99C	XRN1-BGHLV37-100C
Sample_Name_Alias
Index Well Position	S15	S16
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	288	310
Peak_Molarity	10.30	10.30
libSampleQC_DNA_Well	DNA_Library_set40/set1/H6.png	DNA_Library_set40/set1/G6.png
RIN	9.2	9.6
libSample_RNA_Well	RNA_Library_set40/set1/E2.png	RNA_Library_set40/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGHLV37-99	BGHLV37-100
RBP	XRN1	XRN1
Batch_ID	BGHLV37	BGHLV37
WB_result	79.800	85.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	952	953

Sequencing Information

	BGHLV37-99	BGHLV37-100
Sample_ID	BGHLV37-99	BGHLV37-100
Sample Name	XRN1-BGHLV37-99C	XRN1-BGHLV37-100C
Pool ID	Pool-180109	Pool-180109
LocalServer_folder	set40_H	set40_H
total_reads	76,225,712	65,040,576
total_aligned_reads	65,829,282	57,663,402
unique_aligned_reads	61,176,676	53,702,958
percent_uniqueAligned	0.80257	0.82568
correlation_replicates	0.996824	0.996824
spikein_reads	26,768	29,622
percent_spikeins	0.00035	0.00046
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	355	356

Data Submission Information

	BGHLV37-99	BGHLV37-99	BGHLV37-99	BGHLV37-99	BGHLV37-99	BGHLV37-99	BGHLV37-100	BGHLV37-100	BGHLV37-100	BGHLV37-100
ENCODE_alias	brenton-graveley:XRN1-BGHLV37-C	brenton-graveley:XRN1-BGHLV37-99C	brenton-graveley:L-XRN1-BGHLV37-99C	brenton-graveley:XRN1-BGHLV37-99C_ATGTCA_ACBYWVANXX_L002_001.R1.fastq.gz	brenton-graveley:XRN1-BGHLV37-99C_ATGTCA_ACBYWVANXX_L002_001.R2.fastq.gz	brenton-graveley:XRN1-BGHLV37-HepG2	brenton-graveley:XRN1-BGHLV37-100C	brenton-graveley:L-XRN1-BGHLV37-100C	brenton-graveley:XRN1-BGHLV37-100C_CCGTCC_ACBYWVANXX_L002_001.R1.fastq.gz	brenton-graveley:XRN1-BGHLV37-100C_CCGTCC_ACBYWVANXX_L002_001.R2.fastq.gz
ENCODE_accession	ENCSR676SDU	ENCBS469EOJ	ENCLB328NIU	ENCFF277QZF	ENCFF951XOY	ENCSR786TDX	ENCBS482SUX	ENCLB415PXJ	ENCFF823IVL	ENCFF775DWO
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	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
Sample_ID	BGHLV37-99	BGHLV37-99	BGHLV37-99	BGHLV37-99	BGHLV37-99	BGHLV37-99	BGHLV37-100	BGHLV37-100	BGHLV37-100	BGHLV37-100
Sample Name	XRN1-BGHLV37-99C	XRN1-BGHLV37-99C	XRN1-BGHLV37-99C	XRN1-BGHLV37-99C	XRN1-BGHLV37-99C	XRN1-BGHLV37-99C	XRN1-BGHLV37-100C	XRN1-BGHLV37-100C	XRN1-BGHLV37-100C	XRN1-BGHLV37-100C
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	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	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV40_biosample_protocol	LV40_library_protocol				LV40_biosample_protocol	LV40_library_protocol
protocol_URL		XRN1-BGHLV37-100C.pdf	L-XRN1-BGHLV37-99C.pdf				XRN1-BGHLV37-99C.pdf	L-XRN1-BGHLV37-100C.pdf
ID	1454	1506	1562	1600	1637	7359	1507	1563	1599	1636

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
XRN1-BGHLV37-99C_ATGTCA_ACBYWVANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	355	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	670
XRN1-BGHLV37-99C_ATGTCA_ACBYWVANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	355	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	712
XRN1-BGHLV37-99C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	355					GRCh38	V40	XRN1-BGHLV37-99C_ATGTCA_ACBYWVANXX_L002_001.R1.fastq.gz,XRN1-BGHLV37-99C_ATGTCA_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23273
XRN1-BGHLV37-99C_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	355					GRCh38	V40	XRN1-BGHLV37-99C/Aligned.sortedByCoord.out.bam		ENCORE2	23307
XRN1-BGHLV37-99C_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	355					GRCh38	V40	XRN1-BGHLV37-99C/Aligned.sortedByCoord.out.bam		ENCORE2	23341
XRN1-BGHLV37-99C_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	355					GRCh38	V40	XRN1-BGHLV37-99C/Aligned.sortedByCoord.out.bam		ENCORE2	23375
XRN1-BGHLV37-99C_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	355					GRCh38	V40	XRN1-BGHLV37-99C/Aligned.sortedByCoord.out.bam		ENCORE2	23409
XRN1-BGHLV37-99C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	355					GRCh38	V40	XRN1-BGHLV37-99C_ATGTCA_ACBYWVANXX_L002_001.R1.fastq.gz,XRN1-BGHLV37-99C_ATGTCA_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23443
XRN1-BGHLV37-100C_CCGTCC_ACBYWVANXX_L002_001.R1.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	356	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	669
XRN1-BGHLV37-100C_CCGTCC_ACBYWVANXX_L002_001.R2.fastq.gz	ENCODE_DATA/set40_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	356	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	711
XRN1-BGHLV37-100C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_H/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	356					GRCh38	V40	XRN1-BGHLV37-100C_CCGTCC_ACBYWVANXX_L002_001.R1.fastq.gz,XRN1-BGHLV37-100C_CCGTCC_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23272
XRN1-BGHLV37-100C_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	356					GRCh38	V40	XRN1-BGHLV37-100C/Aligned.sortedByCoord.out.bam		ENCORE2	23306
XRN1-BGHLV37-100C_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	356					GRCh38	V40	XRN1-BGHLV37-100C/Aligned.sortedByCoord.out.bam		ENCORE2	23340
XRN1-BGHLV37-100C_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	356					GRCh38	V40	XRN1-BGHLV37-100C/Aligned.sortedByCoord.out.bam		ENCORE2	23374
XRN1-BGHLV37-100C_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	356					GRCh38	V40	XRN1-BGHLV37-100C/Aligned.sortedByCoord.out.bam		ENCORE2	23408
XRN1-BGHLV37-100C_quant.sf	ENCODE_DATA/set40_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	356					GRCh38	V40	XRN1-BGHLV37-100C_CCGTCC_ACBYWVANXX_L002_001.R1.fastq.gz,XRN1-BGHLV37-100C_CCGTCC_ACBYWVANXX_L002_001.R2.fastq.gz		ENCORE2	23442