PAN2 RNA-Seq in K562

General Information


RBP	PAN2
Cell_Line	K562
Method	CRISPR
Exp_Name	PAN2-BGKcLV21-K562
ENCODE_series_ID	ENCSR147ZBR
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR204OEJ
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	PAN2-BGKcLV21-33
Rep2	PAN2-BGKcLV21-34
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	21.7
Rep2_qPCR	12.4
Rep1_WB	74.7
Rep2_WB	65.8
Antibody Cat#	A304-882A
Antibody Lot#	lot# 1
Antibody DCC ID	ENCAB164SAK
Status	Released
Project	ENCODE4
ID	71

Experiment Information (Status: Released)

	BGKcLV21-33	BGKcLV21-34
idx	766	767
TRCN#_or_BGC#	BGC#0000528	BGC#0000528
shRNA_or_gRNA_sequence	ATTACCTGTGTTCGGGGCCA	ATTACCTGTGTTCGGGGCCA
PAM	GGG	GGG
Name	PAN2_91	PAN2_91
Sample_ID	BGKcLV21-33	BGKcLV21-34
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	PAN2	PAN2
qPCR_result	21.7	12.4
Ave_qPCR	17.1
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4436	5407
WB_result	74.7	65.8
Ave_WB	70.3
WB_DONE_date	8/31/20	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	09/24/20	09/24/20
repeat_library
Note
ID	4886	4887

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

	BGKcLV21-33	BGKcLV21-34
Sample_ID	BGKcLV21-33	BGKcLV21-34
Sample Name
Sample Name	PAN2-BGKcLV21-33	PAN2-BGKcLV21-34
RBP	PAN2	PAN2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6133	6134

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-33	BGKcLV21-34
Sample #	51	52
Sample Name	PAN2-BGKcLV21-33	PAN2-BGKcLV21-34
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	312	300
Peak_Molarity	146.00	111.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/E6.png	DNA_Library_set45/set1/F6.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set45/set1/E6.png	RNA_Library_set45/set2/F10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV21-33	BGKcLV21-34
RBP	PAN2	PAN2
Batch_ID	BGKcLV21	BGKcLV21
WB_result	74.700	65.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	825	826

Sequencing Information

	BGKcLV21-33	BGKcLV21-34
Sample_ID	BGKcLV21-33	BGKcLV21-34
Sample Name	PAN2-BGKcLV21-33	PAN2-BGKcLV21-34
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	138,597,344	96,142,386
total_aligned_reads	128,323,526	92,888,888
unique_aligned_reads	117,160,324	84,873,662
percent_uniqueAligned	0.84533	0.88279
correlation_replicates	0.987287	0.987287
spikein_reads	63,958	48,424
percent_spikeins	0.00046	0.00050
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	456	457

Data Submission Information

	BGKcLV21-33	BGKcLV21-33	BGKcLV21-33	BGKcLV21-33	BGKcLV21-33	BGKcLV21-33	BGKcLV21-34	BGKcLV21-34	BGKcLV21-34	BGKcLV21-34
ENCODE_alias	brenton-graveley:PAN2-BGKcLV21	brenton-graveley:PAN2-BGKcLV21-33	brenton-graveley:L-PAN2-BGKcLV21-33	brenton-graveley:PAN2-BGKcLV21-33_S45_R1_001.fastq.gz	brenton-graveley:PAN2-BGKcLV21-33_S45_R2_001.fastq.gz	brenton-graveley:PAN2-BGKcLV21-K562	brenton-graveley:PAN2-BGKcLV21-34	brenton-graveley:L-PAN2-BGKcLV21-34	brenton-graveley:PAN2-BGKcLV21-34_S46_R1_001.fastq.gz	brenton-graveley:PAN2-BGKcLV21-34_S46_R2_001.fastq.gz
ENCODE_accession	ENCSR204OEJ	ENCBS024DGO	ENCLB359AWJ	ENCFF261XTK	ENCFF259QEL	ENCSR147ZBR	ENCBS019RRN	ENCLB932JEX	ENCFF829QTC	ENCFF124GGE
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	BGKcLV21-33	BGKcLV21-33	BGKcLV21-33	BGKcLV21-33	BGKcLV21-33	BGKcLV21-33	BGKcLV21-34	BGKcLV21-34	BGKcLV21-34	BGKcLV21-34
Sample Name	PAN2-BGKcLV21-33	PAN2-BGKcLV21-33	PAN2-BGKcLV21-33	PAN2-BGKcLV21-33	PAN2-BGKcLV21-33	PAN2-BGKcLV21-33	PAN2-BGKcLV21-34	PAN2-BGKcLV21-34	PAN2-BGKcLV21-34	PAN2-BGKcLV21-34
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
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		PAN2-BGKcLV21-33.pdf	L-PAN2-BGKcLV21-33.pdf				PAN2-BGKcLV21-34.pdf	L-PAN2-BGKcLV21-34.pdf
ID	2112	2179	2249	2319	2389	7277	2180	2250	2320	2390

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-BGKcLV21-33_S45_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	456	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1240
PAN2-BGKcLV21-33_S45_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	456	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1290
PAN2-BGKcLV21-33_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	456					GRCh38	V40	PAN2-BGKcLV21-33_S45_R1_001.filtered.trimmed.paired.fastq.gz,PAN2-BGKcLV21-33_S45_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25233
PAN2-BGKcLV21-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	456					GRCh38	V40	PAN2-BGKcLV21-33_S45_R1_001.filtered.trimmed.paired.fastq.gz,PAN2-BGKcLV21-33_S45_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27187
PAN2-BGKcLV21-33_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	456					GRCh38	V40	PAN2-BGKcLV21-33/Aligned.sortedByCoord.out.bam		ENCORE2	27237
PAN2-BGKcLV21-33_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	456					GRCh38	V40	PAN2-BGKcLV21-33/Aligned.sortedByCoord.out.bam		ENCORE2	27287
PAN2-BGKcLV21-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	456					GRCh38	V40	PAN2-BGKcLV21-33/Aligned.sortedByCoord.out.bam		ENCORE2	27337
PAN2-BGKcLV21-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	456					GRCh38	V40	PAN2-BGKcLV21-33/Aligned.sortedByCoord.out.bam		ENCORE2	27387
PAN2-BGKcLV21-34_S46_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	457	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1241
PAN2-BGKcLV21-34_S46_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	457	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1291
PAN2-BGKcLV21-34_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	457					GRCh38	V40	PAN2-BGKcLV21-34_S46_R1_001.filtered.trimmed.paired.fastq.gz,PAN2-BGKcLV21-34_S46_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25234
PAN2-BGKcLV21-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	457					GRCh38	V40	PAN2-BGKcLV21-34_S46_R1_001.filtered.trimmed.paired.fastq.gz,PAN2-BGKcLV21-34_S46_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27188
PAN2-BGKcLV21-34_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	457					GRCh38	V40	PAN2-BGKcLV21-34/Aligned.sortedByCoord.out.bam		ENCORE2	27238
PAN2-BGKcLV21-34_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	457					GRCh38	V40	PAN2-BGKcLV21-34/Aligned.sortedByCoord.out.bam		ENCORE2	27288
PAN2-BGKcLV21-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	457					GRCh38	V40	PAN2-BGKcLV21-34/Aligned.sortedByCoord.out.bam		ENCORE2	27338
PAN2-BGKcLV21-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	457					GRCh38	V40	PAN2-BGKcLV21-34/Aligned.sortedByCoord.out.bam		ENCORE2	27388