XRN1 RNA-Seq in K562

General Information


RBP	XRN1
Cell_Line	K562
Method	shRNA
Exp_Name	XRN1-BGKLV38-K562
ENCODE_series_ID	ENCSR375PNW
Batch_ID	BGKLV38
Pool ID	Pool-180316
Local_Set_Name	set40_K
ENCODE_KD_Exp_ID	ENCSR949RMX
ENCODE_CN_Exp_ID	ENCSR260BQC
Rep1	XRN1-BGKLV38-129C
Rep2	XRN1-BGKLV38-130C
CN1	NT-BGKLV38-1C
CN2	NT-BGKLV38-2C
Rep1_qPCR	58.1
Rep2_qPCR	46.4
Rep1_WB	91.5
Rep2_WB	93.8
Antibody Cat#	A300-443A
Antibody Lot#	A300-443A
Antibody DCC ID	ENCAB231MQI
Status	Released
Project	ENCODE4
ID	279

Experiment Information (Status: Released)

	BGKLV38-129	BGKLV38-130
idx	900	901
TRCN#_or_BGC#	TRCN0000049674	TRCN0000049674
shRNA_or_gRNA_sequence	GCTGGTATTATCCTTATCATT	GCTGGTATTATCCTTATCATT
PAM
Name	XRN1	XRN1
Sample_ID	BGKLV38-129	BGKLV38-130
transduction_Date	9/15/16	9/15/16
days
RBP_name	XRN1	XRN1
qPCR_result	58.1	46.4
Ave_qPCR	52.3
RT-qPCR_primer-F	ggtgaaagagcatcagattcc
RT-qPCR_primer-R	tcattaggatgggagcactg
protein_conc	3028	3451
WB_result	91.5	93.8
Ave_WB	92.7
WB_DONE_date	9/30/16	wes
MW	194kDa
IP	1	1
antibody_Cat#	A300-443A	A300-443A
Antibody DCC ID	ENCAB231MQI	ENCAB231MQI
submitted_to_DCC_date	10/26/16
Rep1_TPM	0	0
Rep2_TPM	0	0
Action
Library_start_date	12/19/17	12/19/17
repeat_library
Note
ID	999	1000

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

	BGKLV38-129	BGKLV38-130
Sample_ID	BGKLV38-129	BGKLV38-130
Sample Name
Sample Name	XRN1-BGKLV38-129C	XRN1-BGKLV38-130C
RBP	XRN1	XRN1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6483	6484

Library-Prep
Sequencing

Library-Prep Information

	BGKLV38-129	BGKLV38-130
Sample #	67	68
Sample Name	XRN1-BGKLV38-129C	XRN1-BGKLV38-130C
Sample_Name_Alias
Index Well Position	S22	S23
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	300	295
Peak_Molarity	27.60	20.10
libSampleQC_DNA_Well	DNA_Library_set40/set1/E10.png	DNA_Library_set40/set1/F10.png
RIN	9.1	9.2
libSample_RNA_Well	RNA_Library_set40/set1/E5.png	RNA_Library_set40/set1/F5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-01-02	2018-01-02
Sample_ID	BGKLV38-129	BGKLV38-130
RBP	XRN1	XRN1
Batch_ID	BGKLV38	BGKLV38
WB_result	91.500	93.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	C	C
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	990	991

Sequencing Information

	BGKLV38-129	BGKLV38-129	BGKLV38-130	BGKLV38-130
Sample_ID	BGKLV38-129	BGKLV38-129	BGKLV38-130	BGKLV38-130
Sample Name	XRN1-BGKLV38-129C	XRN1-BGKLV38-129C	XRN1-BGKLV38-130C	XRN1-BGKLV38-130C
Pool ID	Pool-180109	Pool-180316	Pool-180109	Pool-180316
LocalServer_folder	set40_K	set40_K	set40_K	set40_K
total_reads	19,581,176	54,429,954	24,267,944	35,109,078
total_aligned_reads	17,120,396	47,378,100	20,593,190	30,006,238
unique_aligned_reads	15,344,016	42,900,336	18,648,600	27,120,012
percent_uniqueAligned	0.78361	0.78818	0.76845	0.77245
correlation_replicates	0.989610		0.989610
spikein_reads	7,028	19,622	6,780	10,170
percent_spikeins	0.00036	0.00036	0.00028	0.00029
original_ReadLength	100	100	100	100
QC_Status	Submitted	Submitted	Submitted	Submitted
ID	393	410	394	411

Data Submission Information

	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-130	BGKLV38-130	BGKLV38-130	BGKLV38-130	BGKLV38-130	BGKLV38-130
ENCODE_alias	brenton-graveley:XRN1-BGKLV38-C	brenton-graveley:XRN1-BGKLV38-129C	brenton-graveley:L-XRN1-BGKLV38-129C	brenton-graveley:XRN1-BGKLV38-129C_CGTACG_ACBYWVANXX_L006_001.R1.fastq.gz	brenton-graveley:XRN1-BGKLV38-129C_CGTACG_AHFKCFBCX2_L002_001.R1.fastq.gz	brenton-graveley:XRN1-BGKLV38-129C_CGTACG_ACBYWVANXX_L006_001.R2.fastq.gz	brenton-graveley:XRN1-BGKLV38-129C_CGTACG_AHFKCFBCX2_L002_001.R2.fastq.gz	brenton-graveley:XRN1-BGKLV38-K562	brenton-graveley:XRN1-BGKLV38-130C	brenton-graveley:L-XRN1-BGKLV38-130C	brenton-graveley:XRN1-BGKLV38-130C_GAGTGG_ACBYWVANXX_L006_001.R1.fastq.gz	brenton-graveley:XRN1-BGKLV38-130C_GAGTGG_AHFKCFBCX2_L002_001.R1.fastq.gz	brenton-graveley:XRN1-BGKLV38-130C_GAGTGG_ACBYWVANXX_L006_001.R2.fastq.gz	brenton-graveley:XRN1-BGKLV38-130C_GAGTGG_AHFKCFBCX2_L002_001.R2.fastq.gz
ENCODE_accession	ENCSR949RMX	ENCBS735PDF	ENCLB302IVR	ENCFF881WNN	ENCFF480CSX	ENCFF994ZDW	ENCFF372YXH	ENCSR375PNW	ENCBS625KVU	ENCLB256CZL	ENCFF710VBD	ENCFF968XRD	ENCFF235IQE	ENCFF935MWY
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	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-129	BGKLV38-130	BGKLV38-130	BGKLV38-130	BGKLV38-130	BGKLV38-130	BGKLV38-130
Sample Name	XRN1-BGKLV38-129C	XRN1-BGKLV38-129C	XRN1-BGKLV38-129C	XRN1-BGKLV38-129C	XRN1-BGKLV38-129C	XRN1-BGKLV38-129C	XRN1-BGKLV38-129C	XRN1-BGKLV38-129C	XRN1-BGKLV38-130C	XRN1-BGKLV38-130C	XRN1-BGKLV38-130C	XRN1-BGKLV38-130C	XRN1-BGKLV38-130C	XRN1-BGKLV38-130C
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		XRN1-BGKLV38-129C.pdf	L-XRN1-BGKLV38-129C.pdf						XRN1-BGKLV38-130C.pdf	L-XRN1-BGKLV38-130C.pdf
ID	1455	1508	1564	1673	1674	1706	1707	7360	1509	1565	1675	1676	1708	1709

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-BGKLV38-129C_L001_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	393	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE4	23457
XRN1-BGKLV38-129C_L001_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	393	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE4	23466
XRN1-BGKLV38-129C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	393					GRCh38	V40	XRN1-BGKLV38-129C_L001_001.R1.fastq.gz,XRN1-BGKLV38-129C_L001_001.R2.fastq.gz		ENCORE2	23498
XRN1-BGKLV38-129C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	393					GRCh38	V40	XRN1-BGKLV38-129C/Aligned.sortedByCoord.out.bam		ENCORE2	23532
XRN1-BGKLV38-129C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	393					GRCh38	V40	XRN1-BGKLV38-129C/Aligned.sortedByCoord.out.bam		ENCORE2	23566
XRN1-BGKLV38-129C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	393					GRCh38	V40	XRN1-BGKLV38-129C/Aligned.sortedByCoord.out.bam		ENCORE2	23600
XRN1-BGKLV38-129C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	393					GRCh38	V40	XRN1-BGKLV38-129C/Aligned.sortedByCoord.out.bam		ENCORE2	23634
XRN1-BGKLV38-129C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	393					GRCh38	V40	XRN1-BGKLV38-129C_L001_001.R1.fastq.gz,XRN1-BGKLV38-129C_L001_001.R2.fastq.gz		ENCORE2	23668
XRN1-BGKLV38-130C_L001_001.R1.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	394	HiSeq2500	100	paired-ended	1				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R1.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R1.fastq.gz	ENCODE4	23458
XRN1-BGKLV38-130C_L001_001.R2.fastq.gz	ENCODE_DATA/set40_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	394	HiSeq2500	100	paired-ended	2				NT-BGKLV38-1C_GATCAG_ACBYWVANXX_L004_001.R2.fastq.gz,NT-BGKLV38-2C_TAGCTT_ACBYWVANXX_L004_001.R2.fastq.gz	ENCODE4	23467
XRN1-BGKLV38-130C_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	394					GRCh38	V40	XRN1-BGKLV38-130C_L001_001.R1.fastq.gz,XRN1-BGKLV38-130C_L001_001.R2.fastq.gz		ENCORE2	23499
XRN1-BGKLV38-130C_Signal.Unique.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	394					GRCh38	V40	XRN1-BGKLV38-130C/Aligned.sortedByCoord.out.bam		ENCORE2	23533
XRN1-BGKLV38-130C_Signal.Unique.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	394					GRCh38	V40	XRN1-BGKLV38-130C/Aligned.sortedByCoord.out.bam		ENCORE2	23567
XRN1-BGKLV38-130C_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	394					GRCh38	V40	XRN1-BGKLV38-130C/Aligned.sortedByCoord.out.bam		ENCORE2	23601
XRN1-BGKLV38-130C_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set40_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	394					GRCh38	V40	XRN1-BGKLV38-130C/Aligned.sortedByCoord.out.bam		ENCORE2	23635
XRN1-BGKLV38-130C_quant.sf	ENCODE_DATA/set40_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	394					GRCh38	V40	XRN1-BGKLV38-130C_L001_001.R1.fastq.gz,XRN1-BGKLV38-130C_L001_001.R2.fastq.gz		ENCORE2	23669