A second integrated patchMPRA library tested 24 regulatory sequences, including 13 literature-validated CRSs and 11 CRSs from Library 1, with Hsp68 and MinP promoter variants across 14 K562 landing-pad locations. The table reports published log2(RNA/DNA) expression values for each CRS–landing-pad–promoter combination across three biological replicates, joined to the source library-composition annotations.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0004
Reference genome
hg19
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The Library 2 pGL transfer constructs used Cre-lox cassette exchange into 14 mapped K562 landing pads. It contained 13 literature-validated CRSs amplified from the K562 genome and 11 CRSs from Library 1; each CRS–promoter combination was represented by 25 cBCs. Barcoded Hsp68:dsRed and MinP:dsRed promoter cassettes were compared, and three biological electroporation replicates were measured by barcode sequencing. Activity values are the source log2(RNA/DNA) values and the supplied mean across available biological replicates.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (18 of 18)
Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
Page 1 · 50 rows · More results available
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 18 definitions
element_id
Unique composite identifier formed from genomic coordinate, landing pad, and promoter.
library_component
Package classification as First-library CRS or Literature-validated CRS based on the composition-table reference.
genomic_coordinate
Human genomic interval for the tested CRS, as reported by the source workbook.
sequence_length
Length of the tested CRS in base pairs.
landing_pad
Mapped genomic landing-pad clone label, LP2–LP15 as present in the source table.
promoter
Minimal promoter fused to the dsRed reporter: Hsp68 or MinP.
enhancer_activity_tested_in_mice
Source composition-table flag indicating prior enhancer activity testing in mouse assays.
expressed_in_blood_cells
Source composition-table flag indicating expression in blood cells.
k562_segmentation
Source K562 segmentation annotation for the CRS.
reference
Source composition-table literature reference or ‘This study, 39’ label.
notes
Source composition-table notes, including mouse lift-over annotations where present.
Publisher-supplied mean log2(RNA/DNA) expression across available biological replicates.
replicate_sd
Sample standard deviation of the available replicate expression values.
n_observed_replicates
Number of finite biological-replicate values used for the row; retained rows have at least two.
qc_status
Package QC label; all retained rows passed the minimum 2-of-3 biological-replicate rule.
Quality control
The same expected-context cBC/gBC barcode filtering and averaged expression strategy was used for the integrated reporter measurements. The source expression table contains 593 CRS–landing-pad–promoter rows across all 24 composition-table loci. For this package, rows were retained only when at least 2 of the 3 biological-replicate expression values were finite; 550 rows passed and 43 single-replicate rows were excluded. Blank replicate values in retained rows indicate an unobserved replicate, while mean_expression is the publisher-supplied mean of the available replicate values.
Curation notes
Supplementary Table 4 contains 24 loci and Supplementary Table 5 contains 593 condition-by-location rows; all 24 loci were successfully joined by normalized coordinate. The 43 rows with only one reported replicate were excluded for reproducibility, while 64 rows with two replicates were retained. This experiment compares regulatory sequence and promoter context across genomic environments and does not provide alternative alleles or rs identifiers.