non-target RNA-Seq in HepG2

General Information

List KD experiments controlled by BGHcLV34-1 and BGHcLV34-2

NT-BGHcLV34-1,NT-BGHcLV34-2:

CPSF3L-BGHcLV34-HepG2

NT-BGHcLV34-1B,NT-BGHcLV34-2B:

RIOK1-BGHcLV34-HepG2

RPS21-BGHcLV34-HepG2

Experiment Information (Status: Submitting)

	BGHcLV34-1	BGHcLV34-2
idx	1071	1072
TRCN#_or_BGC#
shRNA_or_gRNA_sequence
PAM
Name	non-target	non-target
Sample_ID	BGHcLV34-1	BGHcLV34-2
transduction_Date	3/24/22	3/24/22
days	D6	D6
RBP_name	non-target	non-target
qPCR_result
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	4337
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	06/17/22	06/17/22
repeat_library	06/22/22	06/22/22
Note
ID	7250	7251

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV34-1	BGHcLV34-1	BGHcLV34-2	BGHcLV34-2
Sample_ID	BGHcLV34-1	BGHcLV34-1	BGHcLV34-2	BGHcLV34-2
Sample Name
Sample Name	NT-BGHcLV34-1	NT-BGHcLV34-1B	NT-BGHcLV34-2	NT-BGHcLV34-2B
RBP	non-target	non-target	non-target	non-target
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Submitting	Submitting	Submitting	Submitting
Status_date	2023-04-14	2023-04-14	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	10797	10939	10798	10940

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV34-1	BGHcLV34-1	BGHcLV34-2	BGHcLV34-2
Sample #	1	53	2	54
Sample Name	NT-BGHcLV34-1	NT-BGHcLV34-1B	NT-BGHcLV34-2	NT-BGHcLV34-2B
Sample_Name_Alias
Index Well Position	A01	E07	B01	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-21	2022-06-17	2022-06-21
Lib_ID	Lib-220617	Lib-220621	Lib-220617	Lib-220621
Tecan_Location
Tecan
Tecan_date
Size_bp	286	259	284	267
Peak_Molarity	28.10	30.30	26.50	22.70
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/A5.png	DNA_Library_set54-56/set4/G11.png	DNA_Library_set54-56/set3/B5.png	DNA_Library_set54-56/set4/H11.png
RIN	9.9	9.9	9.8	9.8
libSample_RNA_Well	RNA_Library_set54-56/set2/A1.png	RNA_Library_set54-56/set2/A1.png	RNA_Library_set54-56/set2/B1.png	RNA_Library_set54-56/set2/B1.png
SampleQC_method	TapeStation_2022	TapeStation_2022	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-07-20	2022-06-20	2022-07-20
Sample_ID	BGHcLV34-1	BGHcLV34-1	BGHcLV34-2	BGHcLV34-2
RBP	NT	NT	NT	NT
Batch_ID	BGHcLV34	BGHcLV34	BGHcLV34	BGHcLV34
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	3318	3370	3319	3371

Sequencing Information

	BGHcLV34-1	BGHcLV34-1	BGHcLV34-2	BGHcLV34-2
Sample_ID	BGHcLV34-1	BGHcLV34-1	BGHcLV34-2	BGHcLV34-2
Sample Name	NT-BGHcLV34-1	NT-BGHcLV34-1B	NT-BGHcLV34-2	NT-BGHcLV34-2B
Pool ID	Pool-220720	Pool-220720	Pool-220720	Pool-220720
LocalServer_folder	set54	set54	set54	set54
total_reads	79,060,370	36,418,374	63,689,340	35,220,876
total_aligned_reads	69,137,800	25,133,634	53,160,906	25,261,414
unique_aligned_reads	65,299,794	23,781,164	50,191,846	23,890,408
percent_uniqueAligned	0.82595	0.65300	0.78807	0.67830
correlation_replicates	0.995423	0.995881	0.995423	0.995881
spikein_reads	8,220	4,868	5,962	3,392
percent_spikeins	0.00010	0.00013	0.00009	0.00010
original_ReadLength	101	101	101	101
QC_Status	Submitting	Submitting	Submitting	Submitting
ID	2195	2217	2196	2218

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-BGHcLV34-1B_S23_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2217	HiSeq2000	100	paired-ended	1				ENCORE2	17712
NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2195	HiSeq2000	100	paired-ended	1				ENCORE2	17713
NT-BGHcLV34-1B_S23_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2217	HiSeq2000	100	paired-ended	2				ENCORE2	17716
NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2195	HiSeq2000	100	paired-ended	2				ENCORE2	17717
NT-BGHcLV34-1B_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2217					GRCh38	V40	NT-BGHcLV34-1/Aligned.sortedByCoord.out.bam	ENCORE2	17744
NT-BGHcLV34-1_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2195					GRCh38	V40	NT-BGHcLV34-1B/Aligned.sortedByCoord.out.bam	ENCORE2	17745
NT-BGHcLV34-1B_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2217					GRCh38	V40	NT-BGHcLV34-1/Aligned.sortedByCoord.out.bam	ENCORE2	17794
NT-BGHcLV34-1_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2195					GRCh38	V40	NT-BGHcLV34-1B/Aligned.sortedByCoord.out.bam	ENCORE2	17795
NT-BGHcLV34-1B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2217					GRCh38	V40	NT-BGHcLV34-1/Aligned.sortedByCoord.out.bam	ENCORE2	17844
NT-BGHcLV34-1_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2195					GRCh38	V40	NT-BGHcLV34-1B/Aligned.sortedByCoord.out.bam	ENCORE2	17845
NT-BGHcLV34-1B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2217					GRCh38	V40	NT-BGHcLV34-1/Aligned.sortedByCoord.out.bam	ENCORE2	17894
NT-BGHcLV34-1_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2195					GRCh38	V40	NT-BGHcLV34-1B/Aligned.sortedByCoord.out.bam	ENCORE2	17895
NT-BGHcLV34-1B_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2217					GRCh38	V40	NT-BGHcLV34-1B_S23_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-1B_S23_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	17944
NT-BGHcLV34-1_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2195					GRCh38	V40	NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	17945
NT-BGHcLV34-1B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2217					GRCh38	V40	NT-BGHcLV34-1B_S23_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-1B_S23_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29285
NT-BGHcLV34-1_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2195					GRCh38	V40	NT-BGHcLV34-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-1_S1_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29286
NT-BGHcLV34-2B_S24_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2218	HiSeq2000	100	paired-ended	1				ENCORE2	17714
NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2196	HiSeq2000	100	paired-ended	1				ENCORE2	17715
NT-BGHcLV34-2B_S24_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2218	HiSeq2000	100	paired-ended	2				ENCORE2	17718
NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2196	HiSeq2000	100	paired-ended	2				ENCORE2	17719
NT-BGHcLV34-2B_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2218					GRCh38	V40	NT-BGHcLV34-2/Aligned.sortedByCoord.out.bam	ENCORE2	17746
NT-BGHcLV34-2_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2196					GRCh38	V40	NT-BGHcLV34-2B/Aligned.sortedByCoord.out.bam	ENCORE2	17747
NT-BGHcLV34-2B_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2218					GRCh38	V40	NT-BGHcLV34-2/Aligned.sortedByCoord.out.bam	ENCORE2	17796
NT-BGHcLV34-2_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2196					GRCh38	V40	NT-BGHcLV34-2B/Aligned.sortedByCoord.out.bam	ENCORE2	17797
NT-BGHcLV34-2B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2218					GRCh38	V40	NT-BGHcLV34-2/Aligned.sortedByCoord.out.bam	ENCORE2	17846
NT-BGHcLV34-2_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2196					GRCh38	V40	NT-BGHcLV34-2B/Aligned.sortedByCoord.out.bam	ENCORE2	17847
NT-BGHcLV34-2B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2218					GRCh38	V40	NT-BGHcLV34-2/Aligned.sortedByCoord.out.bam	ENCORE2	17896
NT-BGHcLV34-2_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2196					GRCh38	V40	NT-BGHcLV34-2B/Aligned.sortedByCoord.out.bam	ENCORE2	17897
NT-BGHcLV34-2B_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2218					GRCh38	V40	NT-BGHcLV34-2B_S24_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2B_S24_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	17946
NT-BGHcLV34-2_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2196					GRCh38	V40	NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	17947
NT-BGHcLV34-2B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2218					GRCh38	V40	NT-BGHcLV34-2B_S24_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2B_S24_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29287
NT-BGHcLV34-2_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2196					GRCh38	V40	NT-BGHcLV34-2_S2_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV34-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29288