SYNCRIP RNA-Seq in HepG2

Experiment Information (Status: Sequenced)

	BGHcLV47-79	BGHcLV47-79	BGHcLV47-80	BGHcLV47-80
idx	1683	1685	1684	1686
TRCN#_or_BGC#	BGC#0000104	BGC#0000104	BGC#0000104	BGC#0000104
shRNA_or_gRNA_sequence	GTGGAGTCATGAAGACTTAC	GTGGAGTCATGAAGACTTAC	GTGGAGTCATGAAGACTTAC	GTGGAGTCATGAAGACTTAC
PAM	AGG	AGG	AGG	AGG
Name	SYNCRIP-73-1	SYNCRIP-73-1	SYNCRIP-73-1	SYNCRIP-73-1
Sample_ID	BGHcLV47-79	BGHcLV47-79	BGHcLV47-80	BGHcLV47-80
transduction_Date	1/28/25	1/28/25	1/28/25	1/28/25
days	D6	D6	D6	D6
RBP_name	SYNCRIP	SYNCRIP	SYNCRIP	SYNCRIP
qPCR_result	62.7	62.7	60.5	60.5
Ave_qPCR	61.6	61.6
RT-qPCR_primer-F	GAAAAGCTCAGAGGCAAGCA	GAAAAGCTCAGAGGCAAGCA
RT-qPCR_primer-R	GGGCATATGAGGTGGACCAT	GGGCATATGAGGTGGACCAT
protein_conc	4616	4616	5228	5228
WB_result	77.2	63.9	77.6	69.5
Ave_WB
WB_DONE_date	2/6/25	3/13/26
MW	70kD	70kD
IP	fu's
antibody_Cat#	RN046PW	8588S		LOT# 1
Antibody DCC ID	ENCAB548DAU
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	9872	9874	9873	9875

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SYNCRIP	Product_ID: RN046PW Lot_ID: 001 Source: MBLI Target Name: SYNCRIP-human
SYNCRIP	Product_ID: 8588S Lot_ID: 1 Source: Cell Signaling Technology Target Name: SYNCRIP-human

Experiment Status

	BGHcLV47-79	BGHcLV47-80
Sample_ID	BGHcLV47-79	BGHcLV47-80
Sample Name
Sample Name	SYNCRIP-BGHcLV47-79	SYNCRIP-BGHcLV47-80
RBP	SYNCRIP	SYNCRIP
Cell_Line	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced
Status_date	2025-05-14	2025-05-14
Project	ENCORE2	ENCORE2
Note
ID	14176	14177

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV47-79	BGHcLV47-80
Sample #	29	30
Sample Name	SYNCRIP-BGHcLV47-79	SYNCRIP-BGHcLV47-80
Sample_Name_Alias
Index Well Position	E11	F11
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-04-23	2025-04-23
Lib_ID	Lib-250423	Lib-250423
Tecan_Location
Tecan
Tecan_date
Size_bp	273	268
Peak_Molarity	92.40	85.20
libSampleQC_DNA_Well	DNA_Library_set78/set1/E9.png	DNA_Library_set78/set1/F9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set78/set1/E4.png	RNA_Library_set78/set1/F4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-04-22	2025-04-22
Sample_ID	BGHcLV47-79	BGHcLV47-80
RBP	SYNCRIP	SYNCRIP
Batch_ID	BGHcLV47	BGHcLV47
WB_result	77.200	77.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4740	4741

Sequencing Information

	BGHcLV47-79	BGHcLV47-80
Sample_ID	BGHcLV47-79	BGHcLV47-80
Sample Name	SYNCRIP-BGHcLV47-79	SYNCRIP-BGHcLV47-80
Pool ID	Pool-250422	Pool-250422
LocalServer_folder	set78	set78
total_reads	15,880,530	20,004,803
total_aligned_reads	14,361,335	17,725,641
unique_aligned_reads	13,509,550	16,686,222
percent_uniqueAligned	0.85070	0.83411
correlation_replicates	0.993301	0.993301
spikein_reads	13,000	13,226
percent_spikeins	0.00082	0.00066
original_ReadLength	101	101
QC_Status	ReadyToSubmit	ReadyToSubmit
ID	3443	3444

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
SYNCRIP-BGHcLV47-79_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3443	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32576
SYNCRIP-BGHcLV47-79_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3443	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32610
SYNCRIP-BGHcLV47-79_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3443					GRCh38	V40	SYNCRIP-BGHcLV47-79_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz,SYNCRIP-BGHcLV47-79_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32644
SYNCRIP-BGHcLV47-79_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3443					GRCh38	V40	SYNCRIP-BGHcLV47-79_Aligned.sortedByCoord.out.bam		ENCORE2	32678
SYNCRIP-BGHcLV47-79_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3443					GRCh38	V40	SYNCRIP-BGHcLV47-79_Aligned.sortedByCoord.out.bam		ENCORE2	32712
SYNCRIP-BGHcLV47-79_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3443					GRCh38	V40	SYNCRIP-BGHcLV47-79_Aligned.sortedByCoord.out.bam		ENCORE2	32746
SYNCRIP-BGHcLV47-79_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3443					GRCh38	V40	SYNCRIP-BGHcLV47-79_Aligned.sortedByCoord.out.bam		ENCORE2	32780
SYNCRIP-BGHcLV47-79_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3443					GRCh38	V40	SYNCRIP-BGHcLV47-79_S70_L002_R1_001.filtered.trimmed.paired.fastq.gz,SYNCRIP-BGHcLV47-79_S70_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32814
SYNCRIP-BGHcLV47-80_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3444	NovaSeq6000	100	paired-ended	1				NT-BGHcLV47-1_S42_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32577
SYNCRIP-BGHcLV47-80_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set78/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3444	NovaSeq6000	100	paired-ended	2				NT-BGHcLV47-1_S42_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV47-2_S43_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	32611
SYNCRIP-BGHcLV47-80_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3444					GRCh38	V40	SYNCRIP-BGHcLV47-80_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz,SYNCRIP-BGHcLV47-80_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32645
SYNCRIP-BGHcLV47-80_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3444					GRCh38	V40	SYNCRIP-BGHcLV47-80_Aligned.sortedByCoord.out.bam		ENCORE2	32679
SYNCRIP-BGHcLV47-80_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3444					GRCh38	V40	SYNCRIP-BGHcLV47-80_Aligned.sortedByCoord.out.bam		ENCORE2	32713
SYNCRIP-BGHcLV47-80_Signal.Unique.strand-.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3444					GRCh38	V40	SYNCRIP-BGHcLV47-80_Aligned.sortedByCoord.out.bam		ENCORE2	32747
SYNCRIP-BGHcLV47-80_Signal.Unique.strand+.bw	ENCODE_DATA/set78/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3444					GRCh38	V40	SYNCRIP-BGHcLV47-80_Aligned.sortedByCoord.out.bam		ENCORE2	32781
SYNCRIP-BGHcLV47-80_quant.sf	ENCODE_DATA/set78/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3444					GRCh38	V40	SYNCRIP-BGHcLV47-80_S71_L002_R1_001.filtered.trimmed.paired.fastq.gz,SYNCRIP-BGHcLV47-80_S71_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32815