ALYREF RNA-Seq in HepG2

General Information


RBP	ALYREF
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ALYREF-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	ALYREF-BGHcLV45-5
Rep2	ALYREF-BGHcLV45-6
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	2.5
Rep2_qPCR	27.1
Rep1_WB	54.2
Rep2_WB	62.5
Antibody Cat#	12655S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1616

Experiment Information (Status: Submitting)

	BGHcLV45-5	BGHcLV45-6
idx	1438	1439
TRCN#_or_BGC#	BGC#0001108	BGC#0001108
shRNA_or_gRNA_sequence	GCCGCGCGAGTGAATCGAGG	GCCGCGCGAGTGAATCGAGG
PAM	CGG	CGG
Name	ALYREF_97	ALYREF_97
Sample_ID	BGHcLV45-5	BGHcLV45-6
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	ALYREF	ALYREF
qPCR_result	2.5	27.1
Ave_qPCR	14.8
RT-qPCR_primer-F	CTGAAGGCCATGAAGCAGTA
RT-qPCR_primer-R	TCTGTGACGTGACAAGCTGA
protein_conc	3786	3221
WB_result	54.2	62.5
Ave_WB
WB_DONE_date	10/15/24
MW	27KD
IP
antibody_Cat#	12655S	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9693	9694

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ALYREF	Product_ID: 12655S Lot_ID: 1 Source: Cell Signaling Technology Target Name: ALYREF-human

Experiment Status

	BGHcLV45-5	BGHcLV45-6
Sample_ID	BGHcLV45-5	BGHcLV45-6
Sample Name
Sample Name	ALYREF-BGHcLV45-5	ALYREF-BGHcLV45-6
RBP	ALYREF	ALYREF
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13690	13691

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-5	BGHcLV45-6
Sample #	5	6
Sample Name	ALYREF-BGHcLV45-5	ALYREF-BGHcLV45-6
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	275	280
Peak_Molarity	91.80	75.40
libSampleQC_DNA_Well	DNA_Library_set76/set1/E7.png	DNA_Library_set76/set1/F7.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set76/set1/E1.png	RNA_Library_set76/set1/F1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-5	BGHcLV45-6
RBP	ALYREF	ALYREF
Batch_ID	BGHcLV45	BGHcLV45
WB_result	54.200	62.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4614	4615

Sequencing Information

	BGHcLV45-5	BGHcLV45-6
Sample_ID	BGHcLV45-5	BGHcLV45-6
Sample Name	ALYREF-BGHcLV45-5	ALYREF-BGHcLV45-6
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	25,124,224	27,683,443
total_aligned_reads	20,452,045	23,545,423
unique_aligned_reads	19,225,506	22,123,470
percent_uniqueAligned	0.76522	0.79916
correlation_replicates	0.998679	0.998679
spikein_reads	22,220	26,524
percent_spikeins	0.00088	0.00096
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3325	3326

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
ALYREF-BGHcLV45-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3325	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31814
ALYREF-BGHcLV45-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3325	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31856
ALYREF-BGHcLV45-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3325					GRCh38	V40	ALYREF-BGHcLV45-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALYREF-BGHcLV45-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31898
ALYREF-BGHcLV45-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3325					GRCh38	V40	ALYREF-BGHcLV45-5_Aligned.sortedByCoord.out.bam		ENCORE2	31940
ALYREF-BGHcLV45-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3325					GRCh38	V40	ALYREF-BGHcLV45-5_Aligned.sortedByCoord.out.bam		ENCORE2	31982
ALYREF-BGHcLV45-5_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3325					GRCh38	V40	ALYREF-BGHcLV45-5_Aligned.sortedByCoord.out.bam		ENCORE2	32024
ALYREF-BGHcLV45-5_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3325					GRCh38	V40	ALYREF-BGHcLV45-5_Aligned.sortedByCoord.out.bam		ENCORE2	32066
ALYREF-BGHcLV45-5_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3325					GRCh38	V40	ALYREF-BGHcLV45-5_S5_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALYREF-BGHcLV45-5_S5_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32108
ALYREF-BGHcLV45-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3326	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31815
ALYREF-BGHcLV45-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3326	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31857
ALYREF-BGHcLV45-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3326					GRCh38	V40	ALYREF-BGHcLV45-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALYREF-BGHcLV45-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31899
ALYREF-BGHcLV45-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3326					GRCh38	V40	ALYREF-BGHcLV45-6_Aligned.sortedByCoord.out.bam		ENCORE2	31941
ALYREF-BGHcLV45-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3326					GRCh38	V40	ALYREF-BGHcLV45-6_Aligned.sortedByCoord.out.bam		ENCORE2	31983
ALYREF-BGHcLV45-6_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3326					GRCh38	V40	ALYREF-BGHcLV45-6_Aligned.sortedByCoord.out.bam		ENCORE2	32025
ALYREF-BGHcLV45-6_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3326					GRCh38	V40	ALYREF-BGHcLV45-6_Aligned.sortedByCoord.out.bam		ENCORE2	32067
ALYREF-BGHcLV45-6_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3326					GRCh38	V40	ALYREF-BGHcLV45-6_S6_L001_R1_001.filtered.trimmed.paired.fastq.gz,ALYREF-BGHcLV45-6_S6_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32109