F11R RNA-Seq in K562

General Information


RBP	F11R
Cell_Line	K562
Method	CRISPR
Exp_Name	F11R-BGKcLV40-K562
ENCODE_series_ID
Batch_ID	BGKcLV40
Pool ID	Pool-231226
Local_Set_Name	set67
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	F11R-BGKcLV40-43
Rep2	F11R-BGKcLV40-44
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	60.1
Rep2_qPCR	57.7
Rep1_WB	92.9
Rep2_WB	92.6
Antibody Cat#	A302-891A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1369

Experiment Information (Status: Submitting)

	BGKcLV40-43	BGKcLV40-44
idx	0	0
TRCN#_or_BGC#	BGC#0001009	BGC#0001009
shRNA_or_gRNA_sequence	GGACAAAGGCGCAAGTCGAG	GGACAAAGGCGCAAGTCGAG
PAM	AGG	AGG
Name	F11R_94	F11R_94
Sample_ID	BGKcLV40-43	BGKcLV40-44
transduction_Date	10/31/23	10/31/23
days	D6	D6
RBP_name	F11R	F11R
qPCR_result	60.1	57.7
Ave_qPCR	58.9
RT-qPCR_primer-F	gggacacccatgacttcaaa
RT-qPCR_primer-R	accagatgccaaaaaccaag
protein_conc	4012	3965
WB_result	92.9	92.6
Ave_WB	92.7
WB_DONE_date	11/8/23
MW	33kd
IP
antibody_Cat#	A302-891A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	1/4/24
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5722	5723

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
F11R	Product_ID: A302-891A Lot_ID: 1 Source: Bethyl Labs Target Name: F11R-human

Experiment Status

	BGKcLV40-43	BGKcLV40-44
Sample_ID	BGKcLV40-43	BGKcLV40-44
Sample Name
Sample Name	F11R-BGKcLV40-43	F11R-BGKcLV40-44
RBP	F11R	F11R
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12782	12783

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-43	BGKcLV40-44
Sample #	29	30
Sample Name	F11R-BGKcLV40-43	F11R-BGKcLV40-44
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-12-19	2023-12-19
Lib_ID	Lib-231219	Lib-231219
Tecan_Location
Tecan
Tecan_date
Size_bp	296	286
Peak_Molarity	54.70	67.00
libSampleQC_DNA_Well	DNA_Library_set67/set1/E10.png	DNA_Library_set67/set1/F10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/E4.png	RNA_Library_set67/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-43	BGKcLV40-44
RBP	F11R	F11R
Batch_ID	BGKcLV40	BGKcLV40
WB_result	92.900	92.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4166	4167

Sequencing Information

	BGKcLV40-43	BGKcLV40-44
Sample_ID	BGKcLV40-43	BGKcLV40-44
Sample Name	F11R-BGKcLV40-43	F11R-BGKcLV40-44
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	38,235,845	29,929,826
total_aligned_reads	33,779,731	24,705,384
unique_aligned_reads	31,064,906	22,659,769
percent_uniqueAligned	0.81246	0.75710
correlation_replicates	0.998527	0.998527
spikein_reads	4,008	8,528
percent_spikeins	0.00010	0.00028
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2821	2822

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
F11R-BGKcLV40-43_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2821	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28167
F11R-BGKcLV40-43_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2821	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28211
F11R-BGKcLV40-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2821					GRCh38	V40	F11R-BGKcLV40-43_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,F11R-BGKcLV40-43_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28255
F11R-BGKcLV40-43_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2821					GRCh38	V40	F11R-BGKcLV40-43/Aligned.sortedByCoord.out.bam		ENCORE2	28299
F11R-BGKcLV40-43_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2821					GRCh38	V40	F11R-BGKcLV40-43/Aligned.sortedByCoord.out.bam		ENCORE2	28343
F11R-BGKcLV40-43_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2821					GRCh38	V40	F11R-BGKcLV40-43/Aligned.sortedByCoord.out.bam		ENCORE2	28387
F11R-BGKcLV40-43_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2821					GRCh38	V40	F11R-BGKcLV40-43/Aligned.sortedByCoord.out.bam		ENCORE2	28431
F11R-BGKcLV40-43_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2821					GRCh38	V40	F11R-BGKcLV40-43_S29_L001_R1_001.filtered.trimmed.paired.fastq.gz,F11R-BGKcLV40-43_S29_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28475
F11R-BGKcLV40-44_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2822	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28168
F11R-BGKcLV40-44_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2822	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28212
F11R-BGKcLV40-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2822					GRCh38	V40	F11R-BGKcLV40-44_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,F11R-BGKcLV40-44_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28256
F11R-BGKcLV40-44_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2822					GRCh38	V40	F11R-BGKcLV40-44/Aligned.sortedByCoord.out.bam		ENCORE2	28300
F11R-BGKcLV40-44_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2822					GRCh38	V40	F11R-BGKcLV40-44/Aligned.sortedByCoord.out.bam		ENCORE2	28344
F11R-BGKcLV40-44_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2822					GRCh38	V40	F11R-BGKcLV40-44/Aligned.sortedByCoord.out.bam		ENCORE2	28388
F11R-BGKcLV40-44_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2822					GRCh38	V40	F11R-BGKcLV40-44/Aligned.sortedByCoord.out.bam		ENCORE2	28432
F11R-BGKcLV40-44_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2822					GRCh38	V40	F11R-BGKcLV40-44_S30_L001_R1_001.filtered.trimmed.paired.fastq.gz,F11R-BGKcLV40-44_S30_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28476