PCF11 RNA-Seq in K562

General Information


RBP	PCF11
Cell_Line	K562
Method	CRISPR
Exp_Name	PCF11-BGKcLV37-K562
ENCODE_series_ID
Batch_ID	BGKcLV37
Pool ID	Pool-230130
Local_Set_Name	set55
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	PCF11-BGKcLV37-29
Rep2	PCF11-BGKcLV37-30
CN1	NT-BGKcLV37-1
CN2	NT-BGKcLV37-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	67.1
Rep2_WB	60.1
Antibody Cat#	A303-706A
Antibody Lot#	lot # 1
Antibody DCC ID	NO ID
Status	Submitted
Project	ENCORE2
ID	1056

Experiment Information (Status: Submitting)

	BGKcLV37-29	BGKcLV37-30
idx	1381	1382
TRCN#_or_BGC#	BGC#0001045	BGC#0001045
shRNA_or_gRNA_sequence	CGATGACTGATAATCCCGAC	CGATGACTGATAATCCCGAC
PAM	AGG	AGG
Name	PCF11_98	PCF11_98
Sample_ID	BGKcLV37-29	BGKcLV37-30
transduction_Date	9/20/22	9/20/22
days	D6	D6
RBP_name	PCF11	PCF11
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	actggcattatcggcaaaat
RT-qPCR_primer-R	cccgttcttccagatcagc
protein_conc	1658	1799
WB_result	67.1	60.1
Ave_WB	63.6
WB_DONE_date	9/27/22,9/28/22,12/1	JESS,licor
MW	173kd
IP
antibody_Cat#	A303-706A	lot # 1
Antibody DCC ID	NO ID
submitted_to_DCC_date	8/29/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5533	5534

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PCF11	Product_ID: A303-706A Lot_ID: 1 Source: Bethyl Labs Target Name: PCF11-human

Experiment Status

	BGKcLV37-29	BGKcLV37-30
Sample_ID	BGKcLV37-29	BGKcLV37-30
Sample Name
Sample Name	PCF11-BGKcLV37-29	PCF11-BGKcLV37-30
RBP	PCF11	PCF11
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	11096	11097

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV37-29	BGKcLV37-30
Sample #	35	36
Sample Name	PCF11-BGKcLV37-29	PCF11-BGKcLV37-30
Sample_Name_Alias
Index Well Position	C05	D05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-01-13	2023-01-13
Lib_ID	Lib-230113	Lib-230113
Tecan_Location
Tecan
Tecan_date
Size_bp	308	302
Peak_Molarity	34.30	53.40
libSampleQC_DNA_Well	DNA_Library_set54-56/set1/C5.png	DNA_Library_set54-56/set1/D5.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set54-56/set1/C5.png	RNA_Library_set54-56/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-01-27	2023-01-27
Sample_ID	BGKcLV37-29	BGKcLV37-30
RBP	PCF11	PCF11
Batch_ID	BGKcLV37	BGKcLV37
WB_result	67.100	60.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3406	3407

Sequencing Information

	BGKcLV37-29	BGKcLV37-30
Sample_ID	BGKcLV37-29	BGKcLV37-30
Sample Name	PCF11-BGKcLV37-29	PCF11-BGKcLV37-30
Pool ID	Pool-230130	Pool-230130
LocalServer_folder	set55	set55
total_reads	84,275,936	45,244,137
total_aligned_reads	78,105,265	43,265,876
unique_aligned_reads	72,477,047	40,103,287
percent_uniqueAligned	0.86000	0.88638
correlation_replicates	0.996790	0.996790
spikein_reads	7,280	3,660
percent_spikeins	0.00009	0.00008
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2279	2280

Data Submission Information DCC submission information was not avaliable

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
PCF11-BGKcLV37-29_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2279	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8396
PCF11-BGKcLV37-29_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2279	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8446
PCF11-BGKcLV37-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2279					GRCh38	V40	PCF11-BGKcLV37-29_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCF11-BGKcLV37-29_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25637
PCF11-BGKcLV37-29_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2279					GRCh38	V40	PCF11-BGKcLV37-29/Aligned.sortedByCoord.out.bam		ENCORE2	25687
PCF11-BGKcLV37-29_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2279					GRCh38	V40	PCF11-BGKcLV37-29/Aligned.sortedByCoord.out.bam		ENCORE2	25737
PCF11-BGKcLV37-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2279					GRCh38	V40	PCF11-BGKcLV37-29/Aligned.sortedByCoord.out.bam		ENCORE2	25787
PCF11-BGKcLV37-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2279					GRCh38	V40	PCF11-BGKcLV37-29/Aligned.sortedByCoord.out.bam		ENCORE2	25837
PCF11-BGKcLV37-29_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2279					GRCh38	V40	PCF11-BGKcLV37-29_S35_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCF11-BGKcLV37-29_S35_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25887
PCF11-BGKcLV37-30_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2280	NovaSeq6000	100	paired-ended	1				NT-BGKcLV37-1_S21_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8397
PCF11-BGKcLV37-30_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set55/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2280	NovaSeq6000	100	paired-ended	2				NT-BGKcLV37-1_S21_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV37-2_S22_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8447
PCF11-BGKcLV37-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2280					GRCh38	V40	PCF11-BGKcLV37-30_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCF11-BGKcLV37-30_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25638
PCF11-BGKcLV37-30_Signal.Unique.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2280					GRCh38	V40	PCF11-BGKcLV37-30/Aligned.sortedByCoord.out.bam		ENCORE2	25688
PCF11-BGKcLV37-30_Signal.Unique.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2280					GRCh38	V40	PCF11-BGKcLV37-30/Aligned.sortedByCoord.out.bam		ENCORE2	25738
PCF11-BGKcLV37-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2280					GRCh38	V40	PCF11-BGKcLV37-30/Aligned.sortedByCoord.out.bam		ENCORE2	25788
PCF11-BGKcLV37-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set55/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2280					GRCh38	V40	PCF11-BGKcLV37-30/Aligned.sortedByCoord.out.bam		ENCORE2	25838
PCF11-BGKcLV37-30_quant.sf	ENCODE_DATA/set55/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2280					GRCh38	V40	PCF11-BGKcLV37-30_S36_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCF11-BGKcLV37-30_S36_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25888