non-target RNA-Seq in HepG2

General Information

List KD experiments controlled by BGHcLV49-1 and BGHcLV49-2

NT-BGHcLV49-1,NT-BGHcLV49-2:No KD experiments controlled by NT-BGHcLV49-1 and NT-BGHcLV49-2 are available on the database

NT-BGHcLV49-1B,NT-BGHcLV49-2B:No KD experiments controlled by NT-BGHcLV49-1B and NT-BGHcLV49-2B are available on the database

Experiment Information (Status: Sequenced)

	BGHcLV49-1	BGHcLV49-2
idx	1698	1699
TRCN#_or_BGC#	BGC#0000000	BGC#0000000
shRNA_or_gRNA_sequence	CAGTCGGGCGTCATCATGAT	CAGTCGGGCGTCATCATGAT
PAM
Name	non-target	non-target
Sample_ID	BGHcLV49-1	BGHcLV49-2
transduction_Date	6/6/25	6/6/25
days	D6	D6
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	5199
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
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	9887	9888

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV49-1	BGHcLV49-1	BGHcLV49-2	BGHcLV49-2
Sample_ID	BGHcLV49-1	BGHcLV49-1	BGHcLV49-2	BGHcLV49-2
Sample Name
Sample Name	NT-BGHcLV49-1	NT-BGHcLV49-1	NT-BGHcLV49-2	NT-BGHcLV49-2
RBP	non-target	non-target	non-target	non-target
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Sequenced	Sequenced	Sequenced	Sequenced
Status_date	2025-10-30	2025-10-30	2025-10-30	2025-10-30
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	14326	14446	14327	14447

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV49-1	BGHcLV49-1	BGHcLV49-2	BGHcLV49-2
Sample #	23	69	24	70
Sample Name	NT-BGHcLV49-1	NT-BGHcLV49-1B	NT-BGHcLV49-2	NT-BGHcLV49-2B
Sample_Name_Alias
Index Well Position	A04	G09	B04	H09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2025-08-20	2025-09-11	2025-08-20	2025-09-11
Lib_ID	Lib-250820	Lib-250911	Lib-250820	Lib-250911
Tecan_Location
Tecan
Tecan_date
Size_bp	262	279	263	271
Peak_Molarity	60.70	98.20	89.40	93.40
libSampleQC_DNA_Well	DNA_Library_set81/set1/A1.png	DNA_Library_set81/set2/G12.png	DNA_Library_set81/set1/B1.png	DNA_Library_set81/set2/H12.png
RIN	10.0	10.0	9.9	9.9
libSample_RNA_Well	RNA_Library_set81/set1/A4.png	RNA_Library_set81/set1/A4.png	RNA_Library_set81/set1/B4.png	RNA_Library_set81/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022	TapeStation_2022	TapeStation_2022
SampleQC_date	2025-09-10	2025-09-15	2025-09-10	2025-09-15
Sample_ID	BGHcLV49-1	BGHcLV49-1	BGHcLV49-2	BGHcLV49-2
RBP	NT	NT	NT	NT
Batch_ID	BGHcLV49	BGHcLV49	BGHcLV49	BGHcLV49
WB_result	0.000	0.000	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
ID	4768	4814	4769	4815

Sequencing Information

	BGHcLV49-1	BGHcLV49-1	BGHcLV49-2	BGHcLV49-2
Sample_ID	BGHcLV49-1	BGHcLV49-1	BGHcLV49-2	BGHcLV49-2
Sample Name	NT-BGHcLV49-1	NT-BGHcLV49-1B	NT-BGHcLV49-2	NT-BGHcLV49-2B
Pool ID	Pool-250916	Pool-250916	Pool-250916	Pool-250916
LocalServer_folder	set81	set81	set81	set81
total_reads	24,715,457	22,487,640	35,338,170	19,789,842
total_aligned_reads	20,417,955	20,651,098	29,660,295	18,072,782
unique_aligned_reads	19,179,508	19,447,475	27,919,640	17,019,516
percent_uniqueAligned	0.77601	0.86481	0.79007	0.86001
correlation_replicates	0.995564	0.997914	0.995564	0.997914
spikein_reads	85,526	84,242	129,072	71,910
percent_spikeins	0.00346	0.00375	0.00365	0.00363
original_ReadLength	151	151	151	151
QC_Status	ReadyToSubmit	ReadyToSubmit	ReadyToSubmit	ReadyToSubmit
ID	3495	3539	3496	3540

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	Project	FILE_ID
NT-BGHcLV49-1B_S138_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3495	NovaSeq6000	100	paired-ended	1				ENCORE2	33194
NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3539	NovaSeq6000	100	paired-ended	1				ENCORE2	33195
NT-BGHcLV49-1B_S138_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3495	NovaSeq6000	100	paired-ended	2				ENCORE2	33240
NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3539	NovaSeq6000	100	paired-ended	2				ENCORE2	33241
NT-BGHcLV49-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3495					GRCh38	V40	NT-BGHcLV49-1B_S138_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-1B_S138_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33286
NT-BGHcLV49-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3539					GRCh38	V40	NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33287
NT-BGHcLV49-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3495					GRCh38	V40	NT-BGHcLV49-1B_Aligned.sortedByCoord.out.bam	ENCORE2	33332
NT-BGHcLV49-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3539					GRCh38	V40	NT-BGHcLV49-1_Aligned.sortedByCoord.out.bam	ENCORE2	33333
NT-BGHcLV49-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3495					GRCh38	V40	NT-BGHcLV49-1B_Aligned.sortedByCoord.out.bam	ENCORE2	33378
NT-BGHcLV49-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3539					GRCh38	V40	NT-BGHcLV49-1_Aligned.sortedByCoord.out.bam	ENCORE2	33379
NT-BGHcLV49-1B_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3495					GRCh38	V40	NT-BGHcLV49-1B_Aligned.sortedByCoord.out.bam	ENCORE2	33424
NT-BGHcLV49-1_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3539					GRCh38	V40	NT-BGHcLV49-1_Aligned.sortedByCoord.out.bam	ENCORE2	33425
NT-BGHcLV49-1B_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3495					GRCh38	V40	NT-BGHcLV49-1B_Aligned.sortedByCoord.out.bam	ENCORE2	33470
NT-BGHcLV49-1_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3539					GRCh38	V40	NT-BGHcLV49-1_Aligned.sortedByCoord.out.bam	ENCORE2	33471
NT-BGHcLV49-1B_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3495					GRCh38	V40	NT-BGHcLV49-1B_S138_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-1B_S138_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33516
NT-BGHcLV49-1_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3539					GRCh38	V40	NT-BGHcLV49-1_S111_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-1_S111_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33517
NT-BGHcLV49-2B_S144_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3496	NovaSeq6000	100	paired-ended	1				ENCORE2	33196
NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3540	NovaSeq6000	100	paired-ended	1				ENCORE2	33197
NT-BGHcLV49-2B_S144_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3496	NovaSeq6000	100	paired-ended	2				ENCORE2	33242
NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set81/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3540	NovaSeq6000	100	paired-ended	2				ENCORE2	33243
NT-BGHcLV49-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3496					GRCh38	V40	NT-BGHcLV49-2B_S144_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2B_S144_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33288
NT-BGHcLV49-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3540					GRCh38	V40	NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33289
NT-BGHcLV49-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3496					GRCh38	V40	NT-BGHcLV49-2B_Aligned.sortedByCoord.out.bam	ENCORE2	33334
NT-BGHcLV49-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3540					GRCh38	V40	NT-BGHcLV49-2_Aligned.sortedByCoord.out.bam	ENCORE2	33335
NT-BGHcLV49-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3496					GRCh38	V40	NT-BGHcLV49-2B_Aligned.sortedByCoord.out.bam	ENCORE2	33380
NT-BGHcLV49-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3540					GRCh38	V40	NT-BGHcLV49-2_Aligned.sortedByCoord.out.bam	ENCORE2	33381
NT-BGHcLV49-2B_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3496					GRCh38	V40	NT-BGHcLV49-2B_Aligned.sortedByCoord.out.bam	ENCORE2	33426
NT-BGHcLV49-2_Signal.Unique.strand-.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3540					GRCh38	V40	NT-BGHcLV49-2_Aligned.sortedByCoord.out.bam	ENCORE2	33427
NT-BGHcLV49-2B_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3496					GRCh38	V40	NT-BGHcLV49-2B_Aligned.sortedByCoord.out.bam	ENCORE2	33472
NT-BGHcLV49-2_Signal.Unique.strand+.bw	ENCODE_DATA/set81/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3540					GRCh38	V40	NT-BGHcLV49-2_Aligned.sortedByCoord.out.bam	ENCORE2	33473
NT-BGHcLV49-2B_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3496					GRCh38	V40	NT-BGHcLV49-2B_S144_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2B_S144_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33518
NT-BGHcLV49-2_quant.sf	ENCODE_DATA/set81/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3540					GRCh38	V40	NT-BGHcLV49-2_S136_L008_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV49-2_S136_L008_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	33519