PUF60 RNA-Seq in HepG2

General Information


RBP	PUF60
Cell_Line	HepG2
Method	shRNA
Exp_Name	PUF60-BGHLV23-HepG2
ENCODE_series_ID	ENCSR979YNN
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR648BSC
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	PUF60-BGHLV23-31
Rep2	PUF60-BGHLV23-32
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	79.0
Rep2_qPCR	76.6
Rep1_WB	97.6
Rep2_WB	98.6
Antibody Cat#	A302-817A
Antibody Lot#	A302-817A
Antibody DCC ID	ENCAB280GIW
Status	Released
Project	ENCODE3
ID	547

Experiment Information (Status: Released)

	BGHLV23-31	BGHLV23-32
idx	523	524
TRCN#_or_BGC#	TRCN0000017248	TRCN0000017248
shRNA_or_gRNA_sequence	CGATGACATCAAGAGCGTGTT	CGATGACATCAAGAGCGTGTT
PAM
Name	PUF60	PUF60
Sample_ID	BGHLV23-31	BGHLV23-32
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	PUF60	PUF60
qPCR_result	79.0	76.6
Ave_qPCR	77.8
RT-qPCR_primer-F	GCGTCTACGTGGGCTCTATC
RT-qPCR_primer-R	GGACATGTCGATGCTCTTGA
protein_conc	6342	5293
WB_result	97.6	98.6
Ave_WB	98.1
WB_DONE_date	4/1/2015
MW
IP	1	1
antibody_Cat#	A302-817A	A302-817A
Antibody DCC ID	ENCAB280GIW	ENCAB280GIW
submitted_to_DCC_date	5/6/2015
Rep1_TPM	9.8	0
Rep2_TPM	13	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2604	2605

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PUF60	Product_ID: A302-817A Lot_ID: 1 Source: Bethyl Labs Target Name: PUF60-human

Experiment Status

	BGHLV23-31	BGHLV23-32
Sample_ID	BGHLV23-31	BGHLV23-32
Sample Name	PUF60-BGHLV23-31	PUF60-BGHLV23-32
Sample Name	PUF60-BGHLV23-31	PUF60-BGHLV23-32
RBP	PUF60	PUF60
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	832	833

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-31	BGHLV23-32
Sample #
Sample Name	PUF60-BGHLV23-31	PUF60-BGHLV23-32
Sample_Name_Alias	PUF60-BGHLV23-31	PUF60-BGHLV23-32
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set4/E1.png	DNA_Library_LV20-22-23/set4/F1.png
RIN	9.2	9.7
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/A7.png	RNA_Library_LV22-23-25/set1/B7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-31	BGHLV23-32
RBP	PUF60	PUF60
Batch_ID	BGHLV23	BGHLV23
WB_result	97.600	98.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2520	2521

Sequencing Information

	BGHLV23-31	BGHLV23-32
Sample_ID	BGHLV23-31	BGHLV23-32
Sample Name	PUF60-BGHLV23-31	PUF60-BGHLV23-32
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	51,690,000	54,510,000
total_aligned_reads	44,516,840	47,054,428
unique_aligned_reads	41,974,082	44,291,328
percent_uniqueAligned	0.81203	0.81254
correlation_replicates	0.994074	0.994074
spikein_reads	308,724	278,064
percent_spikeins	0.00597	0.00510
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1142	1143

Data Submission Information

	BGHLV23-31	BGHLV23-31
ENCODE_alias	brenton-graveley:PUF60-BGHLV23	brenton-graveley:PUF60-BGHLV23-HepG2
ENCODE_accession	ENCSR648BSC	ENCSR979YNN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-31	BGHLV23-31
Sample Name	PUF60-BGHLV23-31	PUF60-BGHLV23-31
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2948	6877

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
PUF60-BGHLV23-31_AGTCAA_L006_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1142	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16672
PUF60-BGHLV23-31_AGTCAA_L006_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1142	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16710
PUF60-BGHLV23-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1142					GRCh38	V40	PUF60-BGHLV23-31_AGTCAA_L006_R1_001.fastq.gz,PUF60-BGHLV23-31_AGTCAA_L006_R2_001.fastq.gz		ENCORE2	16748
PUF60-BGHLV23-31_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1142					GRCh38	V40	PUF60-BGHLV23-31/Aligned.sortedByCoord.out.bam		ENCORE2	16786
PUF60-BGHLV23-31_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1142					GRCh38	V40	PUF60-BGHLV23-31/Aligned.sortedByCoord.out.bam		ENCORE2	16824
PUF60-BGHLV23-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1142					GRCh38	V40	PUF60-BGHLV23-31/Aligned.sortedByCoord.out.bam		ENCORE2	16862
PUF60-BGHLV23-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1142					GRCh38	V40	PUF60-BGHLV23-31/Aligned.sortedByCoord.out.bam		ENCORE2	16900
PUF60-BGHLV23-31_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1142					GRCh38	V40	PUF60-BGHLV23-31_AGTCAA_L006_R1_001.fastq.gz,PUF60-BGHLV23-31_AGTCAA_L006_R2_001.fastq.gz		ENCORE2	16938
PUF60-BGHLV23-32_AGTTCC_L006_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1143	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16673
PUF60-BGHLV23-32_AGTTCC_L006_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1143	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16711
PUF60-BGHLV23-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1143					GRCh38	V40	PUF60-BGHLV23-32_AGTTCC_L006_R1_001.fastq.gz,PUF60-BGHLV23-32_AGTTCC_L006_R2_001.fastq.gz		ENCORE2	16749
PUF60-BGHLV23-32_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1143					GRCh38	V40	PUF60-BGHLV23-32/Aligned.sortedByCoord.out.bam		ENCORE2	16787
PUF60-BGHLV23-32_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1143					GRCh38	V40	PUF60-BGHLV23-32/Aligned.sortedByCoord.out.bam		ENCORE2	16825
PUF60-BGHLV23-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1143					GRCh38	V40	PUF60-BGHLV23-32/Aligned.sortedByCoord.out.bam		ENCORE2	16863
PUF60-BGHLV23-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1143					GRCh38	V40	PUF60-BGHLV23-32/Aligned.sortedByCoord.out.bam		ENCORE2	16901
PUF60-BGHLV23-32_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1143					GRCh38	V40	PUF60-BGHLV23-32_AGTTCC_L006_R1_001.fastq.gz,PUF60-BGHLV23-32_AGTTCC_L006_R2_001.fastq.gz		ENCORE2	16939