RYBP RNA-Seq in HepG2

General Information


RBP	RYBP
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RYBP-BGHcLV20-HepG2
ENCODE_series_ID	ENCSR542UKE
Batch_ID	BGHcLV20
Pool ID	Pool-200928
Local_Set_Name	set45_H
ENCODE_KD_Exp_ID	ENCSR439TMT
ENCODE_CN_Exp_ID	ENCSR306EWE
Rep1	RYBP-BGHcLV20-31
Rep2	RYBP-BGHcLV20-32
CN1	NT-BGHcLV20-1
CN2	NT-BGHcLV20-2
Rep1_qPCR	22.0
Rep2_qPCR	11.0
Rep1_WB	87.0
Rep2_WB	86.9
Antibody Cat#	PA5-19943
Antibody Lot#	LOT# UF2796583
Antibody DCC ID	ENCAB686SDS
Status	Released
Project	ENCODE4
ID	80

Experiment Information (Status: Released)

	BGHcLV20-31	BGHcLV20-32
idx	581	582
TRCN#_or_BGC#	BGC#0000489	BGC#0000489
shRNA_or_gRNA_sequence	TAGGCCCCGGCTGAAAAACG	TAGGCCCCGGCTGAAAAACG
PAM	TGG	TGG
Name	RYBP_92	RYBP_92
Sample_ID	BGHcLV20-31	BGHcLV20-32
transduction_Date	12/10/19	12/10/19
days	D6	D6
RBP_name	RYBP	RYBP
qPCR_result	22.0	11.0
Ave_qPCR	16.5
RT-qPCR_primer-F	GGATTGTAGCGTCTGCACCT
RT-qPCR_primer-R	ACCAGCTGAGAATTGATCCG
protein_conc	4803	5592
WB_result	87.0	86.9
Ave_WB	86.9
WB_DONE_date	7/31/20
MW	24.8kDa
IP	Rabbit / I
antibody_Cat#	PA5-19943	LOT# UF2796583
Antibody DCC ID	ENCAB686SDS
submitted_to_DCC_date	12/9/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	6736	6737

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RYBP	Product_ID: PA5-19943 Lot_ID: UCF2796583 Source: Thermo Fisher Target Name: RYBP-human

Experiment Status

	BGHcLV20-31	BGHcLV20-32
Sample_ID	BGHcLV20-31	BGHcLV20-32
Sample Name
Sample Name	RYBP-BGHcLV20-31	RYBP-BGHcLV20-32
RBP	RYBP	RYBP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5821	5822

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV20-31	BGHcLV20-32
Sample #	71	72
Sample Name	RYBP-BGHcLV20-31	RYBP-BGHcLV20-32
Sample_Name_Alias
Index Well Position	A09	B09
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	321	330
Peak_Molarity	121.00	81.80
libSampleQC_DNA_Well	DNA_Library_set45/set1/A9.png	DNA_Library_set45/set1/B9.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set45/set1/A9.png	RNA_Library_set45/set1/B9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGHcLV20-31	BGHcLV20-32
RBP	RYBP	RYBP
Batch_ID	BGHcLV20	BGHcLV20
WB_result	87.000	86.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	845	846

Sequencing Information

	BGHcLV20-31	BGHcLV20-32
Sample_ID	BGHcLV20-31	BGHcLV20-32
Sample Name	RYBP-BGHcLV20-31	RYBP-BGHcLV20-32
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_H	set45_H
total_reads	104,731,144	117,195,134
total_aligned_reads	101,663,034	112,848,524
unique_aligned_reads	95,838,552	106,693,134
percent_uniqueAligned	0.91509	0.91039
correlation_replicates	0.993580	0.993580
spikein_reads	107,036	88,926
percent_spikeins	0.00102	0.00076
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	476	477

Data Submission Information

	BGHcLV20-31	BGHcLV20-31	BGHcLV20-31	BGHcLV20-31	BGHcLV20-31	BGHcLV20-31	BGHcLV20-32	BGHcLV20-32	BGHcLV20-32	BGHcLV20-32
ENCODE_alias	brenton-graveley:RYBP-BGHcLV20	brenton-graveley:RYBP-BGHcLV20-31	brenton-graveley:L-RYBP-BGHcLV20-31	brenton-graveley:RYBP-BGHcLV20-31_S65_R1_001.fastq.gz	brenton-graveley:RYBP-BGHcLV20-31_S65_R2_001.fastq.gz	brenton-graveley:RYBP-BGHcLV20-HepG2	brenton-graveley:RYBP-BGHcLV20-32	brenton-graveley:L-RYBP-BGHcLV20-32	brenton-graveley:RYBP-BGHcLV20-32_S66_R1_001.fastq.gz	brenton-graveley:RYBP-BGHcLV20-32_S66_R2_001.fastq.gz
ENCODE_accession	ENCSR439TMT	ENCBS537DVW	ENCLB155NFZ	ENCFF903MWV	ENCFF864UBU	ENCSR542UKE	ENCBS164VMA	ENCLB506KZL	ENCFF402CUS	ENCFF295CWD
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	BGHcLV20-31	BGHcLV20-31	BGHcLV20-31	BGHcLV20-31	BGHcLV20-31	BGHcLV20-31	BGHcLV20-32	BGHcLV20-32	BGHcLV20-32	BGHcLV20-32
Sample Name	RYBP-BGHcLV20-31	RYBP-BGHcLV20-31	RYBP-BGHcLV20-31	RYBP-BGHcLV20-31	RYBP-BGHcLV20-31	RYBP-BGHcLV20-31	RYBP-BGHcLV20-32	RYBP-BGHcLV20-32	RYBP-BGHcLV20-32	RYBP-BGHcLV20-32
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-03-18	2022-02-04	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2022-02-04	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45H_biosample_protocol	LV45H_library_protocol				LV45H_biosample_protocol	LV45H_library_protocol
protocol_URL		RYBP-BGHcLV20-31.pdf	L-RYBP-BGHcLV20-31.pdf				RYBP-BGHcLV20-32.pdf	L-RYBP-BGHcLV20-32.pdf
ID	2087	2129	2199	2269	2339	7315	2130	2200	2270	2340

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-BGHcLV20-31_S65_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	476	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1322
RYBP-BGHcLV20-31_S65_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	476	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1342
RYBP-BGHcLV20-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	476					GRCh38	V40	RYBP-BGHcLV20-31_S65_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGHcLV20-31_S65_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24863
RYBP-BGHcLV20-31_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	476					GRCh38	V40	RYBP-BGHcLV20-31_S65_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGHcLV20-31_S65_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24883
RYBP-BGHcLV20-31_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	476					GRCh38	V40	RYBP-BGHcLV20-31/Aligned.sortedByCoord.out.bam		ENCORE2	25933
RYBP-BGHcLV20-31_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	476					GRCh38	V40	RYBP-BGHcLV20-31/Aligned.sortedByCoord.out.bam		ENCORE2	25953
RYBP-BGHcLV20-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	476					GRCh38	V40	RYBP-BGHcLV20-31/Aligned.sortedByCoord.out.bam		ENCORE2	25973
RYBP-BGHcLV20-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	476					GRCh38	V40	RYBP-BGHcLV20-31/Aligned.sortedByCoord.out.bam		ENCORE2	25993
RYBP-BGHcLV20-32_S66_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	477	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1323
RYBP-BGHcLV20-32_S66_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	477	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1343
RYBP-BGHcLV20-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	477					GRCh38	V40	RYBP-BGHcLV20-32_S66_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGHcLV20-32_S66_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24864
RYBP-BGHcLV20-32_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	477					GRCh38	V40	RYBP-BGHcLV20-32_S66_R1_001.filtered.trimmed.paired.fastq.gz,RYBP-BGHcLV20-32_S66_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24884
RYBP-BGHcLV20-32_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	477					GRCh38	V40	RYBP-BGHcLV20-32/Aligned.sortedByCoord.out.bam		ENCORE2	25934
RYBP-BGHcLV20-32_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	477					GRCh38	V40	RYBP-BGHcLV20-32/Aligned.sortedByCoord.out.bam		ENCORE2	25954
RYBP-BGHcLV20-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	477					GRCh38	V40	RYBP-BGHcLV20-32/Aligned.sortedByCoord.out.bam		ENCORE2	25974
RYBP-BGHcLV20-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	477					GRCh38	V40	RYBP-BGHcLV20-32/Aligned.sortedByCoord.out.bam		ENCORE2	25994