PAN2 RNA-Seq in HepG2

General Information


RBP	PAN2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	PAN2-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR874MHJ
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR932GTJ
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	PAN2-BGHcLV22-35
Rep2	PAN2-BGHcLV22-36
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	82.1
Rep2_WB	81.6
Antibody Cat#	A304-882A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB164SAK
Status	Released
Project	ENCODE4
ID	45

Experiment Information (Status: Released)

	BGHcLV22-35	BGHcLV22-36
idx	628	629
TRCN#_or_BGC#	BGC#0000527	BGC#0000527
shRNA_or_gRNA_sequence	ATCCTGGACTCACGCACAGG	ATCCTGGACTCACGCACAGG
PAM	GGG	GGG
Name	PAN2_83	PAN2_83
Sample_ID	BGHcLV22-35	BGHcLV22-36
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	PAN2	PAN2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GTGCAGTTTGACATGAATTGGA
RT-qPCR_primer-R	GCTTCAGCCAGCAAGACACT
protein_conc	2193	1888
WB_result	82.1	81.6
Ave_WB	81.9
WB_DONE_date	9/2/20	JESS
MW	135kDa
IP	Rabbit / I
antibody_Cat#	A304-882A	LOT# 1
Antibody DCC ID	ENCAB164SAK
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	8831	8832

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PAN2	Product_ID: A304-882A Lot_ID: 1 Source: Bethyl Labs Target Name: PAN2-human

Experiment Status

	BGHcLV22-35	BGHcLV22-36
Sample_ID	BGHcLV22-35	BGHcLV22-36
Sample Name
Sample Name	PAN2-BGHcLV22-35	PAN2-BGHcLV22-36
RBP	PAN2	PAN2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7383	7384

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-35	BGHcLV22-36
Sample #	19	20
Sample Name	PAN2-BGHcLV22-35	PAN2-BGHcLV22-36
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	289	294
Peak_Molarity	203.00	137.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/C3.png	DNA_Library_set46/set1/D3.png
RIN	9.3	9.4
libSample_RNA_Well	RNA_Library_set46/set1/C11.png	RNA_Library_set46/set1/D11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-35	BGHcLV22-36
RBP	PAN2	PAN2
Batch_ID	BGHcLV22	BGHcLV22
WB_result	82.100	81.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1394	1395

Sequencing Information

	BGHcLV22-35	BGHcLV22-36
Sample_ID	BGHcLV22-35	BGHcLV22-36
Sample Name	PAN2-BGHcLV22-35	PAN2-BGHcLV22-36
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	310,869,358	339,481,780
total_aligned_reads	254,878,710	279,573,792
unique_aligned_reads	238,832,808	261,879,642
percent_uniqueAligned	0.76827	0.77141
correlation_replicates	0.999767	0.999767
spikein_reads	146,148	113,952
percent_spikeins	0.00047	0.00034
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	500	501

Data Submission Information

	BGHcLV22-35	BGHcLV22-35	BGHcLV22-35	BGHcLV22-35	BGHcLV22-35	BGHcLV22-35	BGHcLV22-36	BGHcLV22-36	BGHcLV22-36	BGHcLV22-36
ENCODE_alias	brenton-graveley:PAN2-BGHcLV22	brenton-graveley:PAN2-BGHcLV22-35	brenton-graveley:L-PAN2-BGHcLV22-35	brenton-graveley:PAN2-BGHcLV22-35_ATGTAAGT+CATAGAGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PAN2-BGHcLV22-35_ATGTAAGT+CATAGAGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PAN2-BGHcLV22-HepG2	brenton-graveley:PAN2-BGHcLV22-36	brenton-graveley:L-PAN2-BGHcLV22-36	brenton-graveley:PAN2-BGHcLV22-36_GCACGGAC+TGCGAGAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:PAN2-BGHcLV22-36_GCACGGAC+TGCGAGAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR932GTJ	ENCBS647PKG	ENCLB927SYC	ENCFF269VCT	ENCFF507NAA	ENCSR874MHJ	ENCBS600LVU	ENCLB163WPF	ENCFF913KHI	ENCFF553SFB
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	BGHcLV22-35	BGHcLV22-35	BGHcLV22-35	BGHcLV22-35	BGHcLV22-35	BGHcLV22-35	BGHcLV22-36	BGHcLV22-36	BGHcLV22-36	BGHcLV22-36
Sample Name	PAN2-BGHcLV22-35	PAN2-BGHcLV22-35	PAN2-BGHcLV22-35	PAN2-BGHcLV22-35	PAN2-BGHcLV22-35	PAN2-BGHcLV22-35	PAN2-BGHcLV22-36	PAN2-BGHcLV22-36	PAN2-BGHcLV22-36	PAN2-BGHcLV22-36
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		PAN2-BGHcLV22-35.pdf	L-PAN2-BGHcLV22-35.pdf				PAN2-BGHcLV22-36.pdf	L-PAN2-BGHcLV22-36.pdf
ID	2404	2445	2509	2573	2603	7276	2446	2510	2574	2604

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
PAN2-BGHcLV22-35_ATGTAAGT+CATAGAGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	500	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1366
PAN2-BGHcLV22-35_ATGTAAGT+CATAGAGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	500	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1430
PAN2-BGHcLV22-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	500					GRCh38	V40	PAN2-BGHcLV22-35_ATGTAAGT+CATAGAGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PAN2-BGHcLV22-35_ATGTAAGT+CATAGAGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25269
PAN2-BGHcLV22-35_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	500					GRCh38	V40	PAN2-BGHcLV22-35_ATGTAAGT+CATAGAGT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PAN2-BGHcLV22-35_ATGTAAGT+CATAGAGT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25367
PAN2-BGHcLV22-35_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	500					GRCh38	V40	PAN2-BGHcLV22-35/Aligned.sortedByCoord.out.bam		ENCORE2	26017
PAN2-BGHcLV22-35_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	500					GRCh38	V40	PAN2-BGHcLV22-35/Aligned.sortedByCoord.out.bam		ENCORE2	26047
PAN2-BGHcLV22-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	500					GRCh38	V40	PAN2-BGHcLV22-35/Aligned.sortedByCoord.out.bam		ENCORE2	26077
PAN2-BGHcLV22-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	500					GRCh38	V40	PAN2-BGHcLV22-35/Aligned.sortedByCoord.out.bam		ENCORE2	26107
PAN2-BGHcLV22-36_GCACGGAC+TGCGAGAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	501	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1367
PAN2-BGHcLV22-36_GCACGGAC+TGCGAGAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	501	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1431
PAN2-BGHcLV22-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	501					GRCh38	V40	PAN2-BGHcLV22-36_GCACGGAC+TGCGAGAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PAN2-BGHcLV22-36_GCACGGAC+TGCGAGAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25270
PAN2-BGHcLV22-36_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	501					GRCh38	V40	PAN2-BGHcLV22-36_GCACGGAC+TGCGAGAC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,PAN2-BGHcLV22-36_GCACGGAC+TGCGAGAC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25368
PAN2-BGHcLV22-36_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	501					GRCh38	V40	PAN2-BGHcLV22-36/Aligned.sortedByCoord.out.bam		ENCORE2	26018
PAN2-BGHcLV22-36_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	501					GRCh38	V40	PAN2-BGHcLV22-36/Aligned.sortedByCoord.out.bam		ENCORE2	26048
PAN2-BGHcLV22-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	501					GRCh38	V40	PAN2-BGHcLV22-36/Aligned.sortedByCoord.out.bam		ENCORE2	26078
PAN2-BGHcLV22-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	501					GRCh38	V40	PAN2-BGHcLV22-36/Aligned.sortedByCoord.out.bam		ENCORE2	26108