RYBP RNA-Seq in K562

General Information


RBP	RYBP
Cell_Line	K562
Method	CRISPR
Exp_Name	RYBP-BGKcLV19-K562
ENCODE_series_ID	ENCSR887DWQ
Batch_ID	BGKcLV19
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR607RGV
ENCODE_CN_Exp_ID	ENCSR978MMZ
Rep1	RYBP-BGKcLV19-43
Rep2	RYBP-BGKcLV19-44
CN1	NT-BGKcLV19-1
CN2	NT-BGKcLV19-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	55.2
Rep2_WB	60.8
Antibody Cat#	PA5-19943
Antibody Lot#	UCF2796583
Antibody DCC ID	ENCAB686SDS
Status	Released
Project	ENCODE4
ID	58

Experiment Information (Status: Released)

	BGKcLV19-43	BGKcLV19-44
idx	715	716
TRCN#_or_BGC#	BGC#0000489	BGC#0000489
shRNA_or_gRNA_sequence	TAGGCCCCGGCTGAAAAACG	TAGGCCCCGGCTGAAAAACG
PAM	TGG	TGG
Name	RYBP_92	RYBP_92
Sample_ID	BGKcLV19-43	BGKcLV19-44
transduction_Date	11/6/19	11/6/19
days	Day 6	Day 6
RBP_name	RYBP	RYBP
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	3770	3710
WB_result	55.2	60.8
Ave_WB	58.0
WB_DONE_date	7/31/20
MW	24.8kDa
IP	Rabbit / I
antibody_Cat#	PA5-19943
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	10.5	0
Rep2_TPM	10.9	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4835	4836

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV19-43	BGKcLV19-44
Sample_ID	BGKcLV19-43	BGKcLV19-44
Sample Name
Sample Name	RYBP-BGKcLV19-43	RYBP-BGKcLV19-44
RBP	RYBP	RYBP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5709	5710

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV19-43	BGKcLV19-44
Sample #	23	24
Sample Name	RYBP-BGKcLV19-43	RYBP-BGKcLV19-44
Sample_Name_Alias
Index Well Position	A03	B03
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	305	320
Peak_Molarity	81.10	85.70
libSampleQC_DNA_Well	DNA_Library_set45/set1/A3.png	DNA_Library_set45/set1/B3.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set45/set1/A3.png	RNA_Library_set45/set1/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV19-43	BGKcLV19-44
RBP	RYBP	RYBP
Batch_ID	BGKcLV19	BGKcLV19
WB_result	55.200	60.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	797	798

Sequencing Information

	BGKcLV19-43	BGKcLV19-44
Sample_ID	BGKcLV19-43	BGKcLV19-44
Sample Name	RYBP-BGKcLV19-43	RYBP-BGKcLV19-44
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	101,726,270	160,522,632
total_aligned_reads	94,868,668	148,521,568
unique_aligned_reads	86,823,486	135,874,202
percent_uniqueAligned	0.85350	0.84645
correlation_replicates	0.993070	0.993070
spikein_reads	116,444	131,298
percent_spikeins	0.00114	0.00082
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	428	429

Data Submission Information

	BGKcLV19-43	BGKcLV19-43	BGKcLV19-43	BGKcLV19-43	BGKcLV19-43	BGKcLV19-43	BGKcLV19-44	BGKcLV19-44	BGKcLV19-44	BGKcLV19-44
ENCODE_alias	brenton-graveley:RYBP-BGKcLV19	brenton-graveley:RYBP-BGKcLV19-43	brenton-graveley:L-RYBP-BGKcLV19-43	brenton-graveley:RYBP-BGKcLV19-43_S17_R1_001.fastq.gz	brenton-graveley:RYBP-BGKcLV19-43_S17_R2_001.fastq.gz	brenton-graveley:RYBP-BGKcLV19-K562	brenton-graveley:RYBP-BGKcLV19-44	brenton-graveley:L-RYBP-BGKcLV19-44	brenton-graveley:RYBP-BGKcLV19-44_S18_R1_001.fastq.gz	brenton-graveley:RYBP-BGKcLV19-44_S18_R2_001.fastq.gz
ENCODE_accession	ENCSR607RGV	ENCBS327UNO	ENCLB723AQT	ENCFF499MZM	ENCFF967NWW	ENCSR887DWQ	ENCBS053RXY	ENCLB034QXG	ENCFF126WYX	ENCFF997JAX
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	BGKcLV19-43	BGKcLV19-43	BGKcLV19-43	BGKcLV19-43	BGKcLV19-43	BGKcLV19-43	BGKcLV19-44	BGKcLV19-44	BGKcLV19-44	BGKcLV19-44
Sample Name	RYBP-BGKcLV19-43	RYBP-BGKcLV19-43	RYBP-BGKcLV19-43	RYBP-BGKcLV19-43	RYBP-BGKcLV19-43	RYBP-BGKcLV19-43	RYBP-BGKcLV19-44	RYBP-BGKcLV19-44	RYBP-BGKcLV19-44	RYBP-BGKcLV19-44
Selected	Yes	No	Yes	Yes	Yes	Yes	No	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_library_protocol					LV45K_library_protocol
protocol_URL			L-RYBP-BGKcLV19-43.pdf					L-RYBP-BGKcLV19-44.pdf
ID	2098	2151	2221	2291	2361	7316	2152	2222	2292	2362

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
RYBP-BGKcLV19-43_S17_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	428	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1246
RYBP-BGKcLV19-43_S17_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	428	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1296
RYBP-BGKcLV19-43_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	428					GRCh38	V40	RYBP-BGKcLV19-43_S17_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGKcLV19-43_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25239
RYBP-BGKcLV19-43_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	428					GRCh38	V40	RYBP-BGKcLV19-43_S17_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGKcLV19-43_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27193
RYBP-BGKcLV19-43_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	428					GRCh38	V40	RYBP-BGKcLV19-43/Aligned.sortedByCoord.out.bam		ENCORE2	27243
RYBP-BGKcLV19-43_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	428					GRCh38	V40	RYBP-BGKcLV19-43/Aligned.sortedByCoord.out.bam		ENCORE2	27293
RYBP-BGKcLV19-43_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	428					GRCh38	V40	RYBP-BGKcLV19-43/Aligned.sortedByCoord.out.bam		ENCORE2	27343
RYBP-BGKcLV19-43_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	428					GRCh38	V40	RYBP-BGKcLV19-43/Aligned.sortedByCoord.out.bam		ENCORE2	27393
RYBP-BGKcLV19-44_S18_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	429	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1247
RYBP-BGKcLV19-44_S18_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	429	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1297
RYBP-BGKcLV19-44_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	429					GRCh38	V40	RYBP-BGKcLV19-44_S18_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGKcLV19-44_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25240
RYBP-BGKcLV19-44_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	429					GRCh38	V40	RYBP-BGKcLV19-44_S18_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGKcLV19-44_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27194
RYBP-BGKcLV19-44_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	429					GRCh38	V40	RYBP-BGKcLV19-44/Aligned.sortedByCoord.out.bam		ENCORE2	27244
RYBP-BGKcLV19-44_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	429					GRCh38	V40	RYBP-BGKcLV19-44/Aligned.sortedByCoord.out.bam		ENCORE2	27294
RYBP-BGKcLV19-44_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	429					GRCh38	V40	RYBP-BGKcLV19-44/Aligned.sortedByCoord.out.bam		ENCORE2	27344
RYBP-BGKcLV19-44_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	429					GRCh38	V40	RYBP-BGKcLV19-44/Aligned.sortedByCoord.out.bam		ENCORE2	27394