title: Human meningioma, Frozen [M231]

description: Nanostring nCounter


title: Human meningioma, Frozen [M228]

status: Public on Sep 06 2023

type: RNA

city: San Francisco

first: William

last: Chen

state: CA

address: 1450 3rd Street, HD 402

country: USA

institute: UCSF

description: Nanostring nCounter

hyb_protocol: 200 ng of total RNA per sample was hybridized to barcoded reporter probes and biotin-conjugated capture probes from a custom codeset targeting genes of interest at 65C for 16 hours according to manufacturer instruction. Hybridization mixtures were washed and target/probe complexes were purified and bound to streptavidin coated cartridges.

scan_protocol: Cartridges were scanned on the nCounter Digital Analyzer with a FOV setting of 550

data_processing:
Samples here are unique meningiomas included in the study. Counts were positive control normalized using the spike-in positive control probes in the nSolver solftware, as per recommendations from the manufacturer (Nanostring).
Positive control normalized counts

molecule: total RNA

organism: Homo sapiens

source_name: Human meningioma, Frozen

extract_protocol: Total RNA was extracted from frozen or FFPE meningioma tumor samples using Qiagen AllPrep or Qiagen FFPE RNAeasy kits.

tag: disease

value: meningioma


title: Human meningioma, Frozen [M23]

description: Nanostring nCounter

label_protocol: 200 ng of total RNA per sample was hybridized to barcoded reporter probes and biotin-conjugated capture probes from a custom codeset targeting genes of interest at 65C for 16 hours according to manufacturer instruction. Hybridization mixtures were washed and target/probe complexes were purified and bound to streptavidin coated cartridges.


title: Human meningioma, Frozen [M230]

description: Nanostring nCounter


title: Human meningioma, Frozen [M226]

description: Nanostring nCounter


title: Human meningioma, Frozen [M227]

description: Nanostring nCounter


title: Human meningioma, Frozen [M225]

description: Nanostring nCounter


title: Human meningioma, Frozen [M52]

description: Nanostring nCounter


title: Human meningioma, Frozen [M49]

description: Nanostring nCounter


title: Human meningioma, Frozen [M221]

description: Nanostring nCounter


title: Human meningioma, Frozen [M219]

description: Nanostring nCounter


title: Human meningioma, Frozen [M216]

description: Nanostring nCounter


title: Human meningioma, Frozen [M222]

description: Nanostring nCounter


title: Human meningioma, Frozen [M224]

description: Nanostring nCounter


title: Human meningioma, Frozen [M215]

description: Nanostring nCounter


title: Human meningioma, Frozen [M213]

description: Nanostring nCounter


title: Human meningioma, Frozen [M214]

description: Nanostring nCounter


title: Human meningioma, Frozen [M212]

description: Nanostring nCounter


title: Human meningioma, Frozen [M208]

description: Nanostring nCounter


title: Human meningioma, Frozen [M21]

description: Nanostring nCounter


title: Human meningioma, Frozen [M207]

description: Nanostring nCounter


title: Human meningioma, Frozen [M206]

description: Nanostring nCounter


title: Human meningioma, Frozen [M209]

description: Nanostring nCounter


title: Human meningioma, Frozen [M205]

description: Nanostring nCounter


title: Human meningioma, Frozen [M210]

description: Nanostring nCounter


title: Human meningioma, Frozen [M203]

description: Nanostring nCounter


title: Human meningioma, Frozen [M200]

description: Nanostring nCounter


title: Human meningioma, Frozen [M202]

description: Nanostring nCounter


title: Human meningioma, Frozen [M201]

description: Nanostring nCounter


title: Human meningioma, Frozen [M20]

description: Nanostring nCounter


title: Human meningioma, Frozen [M2]

description: Nanostring nCounter


title: Human meningioma, Frozen [M198]

description: Nanostring nCounter


title: Human meningioma, Frozen [M232]

description: Nanostring nCounter


title: Human meningioma, Frozen [M199]

description: Nanostring nCounter


title: Human meningioma, Frozen [M218]

description: Nanostring nCounter


title: Human meningioma, Frozen [M197]

description: Nanostring nCounter


title: Human meningioma, Frozen [M217]

description: Nanostring nCounter


title: Human meningioma, Frozen [M193]

description: Nanostring nCounter


title: Human meningioma, Frozen [M194]

description: Nanostring nCounter


title: Human meningioma, Frozen [M192]

description: Nanostring nCounter


title: Human meningioma, Frozen [M190]

description: Nanostring nCounter


title: Human meningioma, Frozen [M191]

description: Nanostring nCounter


title: Human meningioma, Frozen [M19]

description: Nanostring nCounter


title: Human meningioma, Frozen [M185]

description: Nanostring nCounter


title: Human meningioma, Frozen [M186]

description: Nanostring nCounter


title: Human meningioma, Frozen [M184]

description: Nanostring nCounter


title: Human meningioma, Frozen [M187]

description: Nanostring nCounter


title: Human meningioma, Frozen [M180]

description: Nanostring nCounter


title: Human meningioma, Frozen [M183]

description: Nanostring nCounter


title: Human meningioma, Frozen [M181]

description: Nanostring nCounter


title: Human meningioma, Frozen [M18]

description: Nanostring nCounter


title: Human meningioma, Frozen [M175]

description: Nanostring nCounter


title: Human meningioma, Frozen [M174]

description: Nanostring nCounter


title: Human meningioma, Frozen [M168]

description: Nanostring nCounter


title: Human meningioma, Frozen [M171]

description: Nanostring nCounter


title: Human meningioma, Frozen [M173]

description: Nanostring nCounter


title: Human meningioma, Frozen [M182]

description: Nanostring nCounter


title: Human meningioma, Frozen [M178]

description: Nanostring nCounter


title: Human meningioma, Frozen [M169]

description: Nanostring nCounter


title: Human meningioma, Frozen [M17]

description: Nanostring nCounter


title: Human meningioma, Frozen [M170]

description: Nanostring nCounter


title: Human meningioma, Frozen [M166]

description: Nanostring nCounter


title: Human meningioma, Frozen [M167]

description: Nanostring nCounter


title: Human meningioma, Frozen [M165]

description: Nanostring nCounter


title: Human meningioma, Frozen [M163]

description: Nanostring nCounter


title: Human meningioma, Frozen [M162]

description: Nanostring nCounter


title: Human meningioma, Frozen [M161]

description: Nanostring nCounter


title: Human meningioma, Frozen [M188]

description: Nanostring nCounter


title: Human meningioma, Frozen [M159]

description: Nanostring nCounter


title: Human meningioma, Frozen [M158]

description: Nanostring nCounter


title: Human meningioma, Frozen [M160]

description: Nanostring nCounter


title: Human meningioma, Frozen [M189]

description: Nanostring nCounter


title: Human meningioma, Frozen [M157]

description: Nanostring nCounter


title: Human meningioma, Frozen [M155]

description: Nanostring nCounter


title: Human meningioma, Frozen [M141]

description: Nanostring nCounter


title: Human meningioma, Frozen [M15]

description: Nanostring nCounter


title: Human meningioma, Frozen [M145]

description: Nanostring nCounter


title: Human meningioma, Frozen [M142]

description: Nanostring nCounter


title: Human meningioma, Frozen [M156]

description: Nanostring nCounter


title: Human meningioma, Frozen [M150]

description: Nanostring nCounter


title: Human meningioma, Frozen [M153]

description: Nanostring nCounter


title: Human meningioma, Frozen [M147]

description: Nanostring nCounter


title: Human meningioma, Frozen [M146]

description: Nanostring nCounter


title: Human meningioma, Frozen [M123]

description: Nanostring nCounter


title: Human meningioma, Frozen [M152]

description: Nanostring nCounter


title: Human meningioma, Frozen [M143]

description: Nanostring nCounter


title: Human meningioma, Frozen [M133]

description: Nanostring nCounter


title: Human meningioma, Frozen [M129]

description: Nanostring nCounter


title: Human meningioma, Frozen [M135]

description: Nanostring nCounter


title: Human meningioma, Frozen [M132]

description: Nanostring nCounter


title: Human meningioma, Frozen [M126]

description: Nanostring nCounter


title: Human meningioma, Frozen [M124]

description: Nanostring nCounter


title: Human meningioma, Frozen [M130]

description: Nanostring nCounter


title: Human meningioma, Frozen [M134]

description: Nanostring nCounter


title: Human meningioma, Frozen [M125]

description: Nanostring nCounter


title: Human meningioma, Frozen [M128]

description: Nanostring nCounter


title: Human meningioma, Frozen [M137]

description: Nanostring nCounter


title: Human meningioma, Frozen [M127]

description: Nanostring nCounter


title: Human meningioma, Frozen [M176]

description: Nanostring nCounter


title: Human meningioma, Frozen [M144]

description: Nanostring nCounter


title: Human meningioma, Frozen [M14]

description: Nanostring nCounter


title: Human meningioma, Frozen [M139]

description: Nanostring nCounter


title: Human meningioma, Frozen [M122]

description: Nanostring nCounter


title: Human meningioma, Frozen [M120]

description: Nanostring nCounter


title: Human meningioma, Frozen [M12]

description: Nanostring nCounter


title: Human meningioma, Frozen [M112]

description: Nanostring nCounter


title: Human meningioma, Frozen [M108]

description: Nanostring nCounter


title: Human meningioma, Frozen [M107]

description: Nanostring nCounter


title: Human meningioma, Frozen [M114]

description: Nanostring nCounter


title: Human meningioma, Frozen [M102]

description: Nanostring nCounter


title: Human meningioma, Frozen [M111]

description: Nanostring nCounter


title: Human meningioma, Frozen [M117]

description: Nanostring nCounter


title: Human meningioma, FFPE [MEN-89]

description: Nanostring SPRINT

source_name: Human meningioma, FFPE


title: Human meningioma, Frozen [M104]

description: Nanostring nCounter


title: Human meningioma, FFPE [MEN-102]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-87]

description: Nanostring SPRINT


title: Human meningioma, Frozen [M103]

description: Nanostring nCounter


title: Human meningioma, Frozen [M110]

description: Nanostring nCounter


title: Human meningioma, FFPE [MEN-101]

description: Nanostring SPRINT


title: Human meningioma, Frozen [M106]

description: Nanostring nCounter


title: Human meningioma, Frozen [M100]

description: Nanostring nCounter


title: Human meningioma, Frozen [M10]

description: Nanostring nCounter


title: Human meningioma, Frozen [1782]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-86]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1662]

description: Nanostring SPRINT


title: Human meningioma, Frozen [M105]

description: Nanostring nCounter


title: Human meningioma, Frozen [1287]

description: Nanostring SPRINT


title: Human meningioma, Frozen [M115]

description: Nanostring nCounter


title: Human meningioma, Frozen [M113]

description: Nanostring nCounter


title: Human meningioma, FFPE [MEN-84]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-85]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-83]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1221]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1795]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-88]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1277]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-81]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-82]

description: Nanostring SPRINT


title: Human meningioma, Frozen [M101]

description: Nanostring nCounter


title: Human meningioma, FFPE [MEN-77]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-78]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-80]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1263]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-76]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-75]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-74]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-99]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-79]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1630]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1219]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1785]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1202]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1181]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-98]

description: Nanostring SPRINT


title: Human meningioma, Frozen [M119]

description: Nanostring nCounter


title: Human meningioma, FFPE [MEN-73]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-70]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-71]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-72]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-69]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1780]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1555]

description: Nanostring SPRINT


title: Human meningioma, Frozen [2141]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1145]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1526]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1242]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1158]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1292]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-64]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1112]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1749]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-65]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-67]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1582]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1572]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1556]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1305]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1339]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1301]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-62]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1617]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-68]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1590]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1136]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1403]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1513]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1340]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1048]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1043]

description: Nanostring SPRINT


title: Human meningioma, Frozen [2688]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1506]

description: Nanostring SPRINT


title: Human meningioma, Frozen [2731]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-54]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1013]

description: Nanostring SPRINT


title: Human meningioma, Frozen [0689C]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-55]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1022]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-53]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-59]

description: Nanostring SPRINT


title: Human meningioma, Frozen [2582]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1614]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-57]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-56]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1473]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1033]

description: Nanostring SPRINT


title: Human meningioma, Frozen [2886]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-60]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-39]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-30]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1440]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-38]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1025]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-42]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1361]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-29]

description: Nanostring SPRINT


title: Human meningioma, Frozen [2447]

description: Nanostring SPRINT


title: Human meningioma, Frozen [2372]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-45]

description: Nanostring SPRINT


title: Human meningioma, Frozen [0634C]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-41]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-32]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-33]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-40]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-34]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1949]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1919]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-43]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-44]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00558]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-47]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-48]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-46]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1029]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-25]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-36]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1890]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1855]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1823]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-50]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-24]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-51]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-27]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-66]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1962]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-26]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-21 B1]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1709]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00932]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-31]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00896]

description: Nanostring SPRINT


title: Human meningioma, FFPE [NU00864]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00825]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00888]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00469]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00528]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-23 A2]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00437]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00268]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00283]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00678]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00957]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00717]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-5]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00591]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00259]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00702]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-8]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00695]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-49]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00898]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00929]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00661]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00619B]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00398]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00692]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-17]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1648]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00954]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00950]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00821]

description: Nanostring SPRINT


title: Fibroblasts, Tek-crexCsf1f/f hypodermis, replicate 6

type: SRA

city: Bethesda

first: Keisuke

last: Nagao

state: MD

address: 10 Center Dr, Bldg 10, 12N240B

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
The FASTQ files data were aligned to mouse genome (mm10) with STAR software (2.6.1c). Gene count of mapped reads was performed via GenomicFeatures and GenomicAlignments tools on R platform and then used as an input for downstream analysis using DESeq2 package
Assembly: mm10
Supplementary files format and content: Excel files containing raw read counts

organism: Mus musculus

source_name: Hypodermal adventitia

extract_protocol:
Back skins from age-matched Csf1f/f and Tek-crexCsf1f/f mice were harvested and hypodermal adventitial was isolated by mechanical force and enzymatic treatments. Cells were liberated after enzymatic digestion of the tissues. Fibroblasts (SYTOX Red- CD45- CD31- Sca-1+ CD34+ Sca1+) were isolated by fluorescence-activated cell sorting (FACS).  Cells were collected in TRIzol LS and RNA was extracted using Direct-zol RNA MicroPrep (Zymo Research) and their transcriptome assessed by RNA-sequencing.
RNA libraries were prepared using a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers Set) (New England BioLabs) according to manufacturer protocol

tag: tissue

value: Hypodermal adventitia

tag: cell type

value: Fibroblasts

tag: genotype

value: Tek-crex Csf1fl/fl

tag: age

value: 8-10 weeks old

tag: treatment

value: No treatment


title: Fibroblasts, Tek-crexCsf1f/f hypodermis, replicate 5


title: Human meningioma, Frozen [NU00803]

description: Nanostring SPRINT


title: Fibroblasts, Tek-crexCsf1f/f hypodermis, replicate 4


title: Human meningioma, Frozen [NU00794]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00368]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00356]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00994]

description: Nanostring SPRINT


title: Fibroblasts, Tek-crexCsf1f/f hypodermis, replicate 2


title: Fibroblasts, control hypodermis, replicate 5


title: Human meningioma, Frozen [NU00604]

description: Nanostring SPRINT


title: Fibroblasts, control hypodermis, replicate 6


title: Fibroblasts, Tek-crexCsf1f/f hypodermis, replicate 3


title: Human meningioma, Frozen [NU00346]

description: Nanostring SPRINT


title: Fibroblasts, Tek-crexCsf1f/f hypodermis, replicate 1


title: Human meningioma, Frozen [NU00877]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-4]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00763]

description: Nanostring SPRINT


title: Fibroblasts, control hypodermis, replicate 4


title: Human meningioma, Frozen [1594]

description: Nanostring SPRINT


title: Fibroblasts, control hypodermis, replicate 3


title: Fibroblasts, control hypodermis, replicate 2


title: Human meningioma, Frozen [NU00867]

description: Nanostring SPRINT


title: Fibroblasts, control hypodermis, replicate 1


title: Human meningioma, Frozen [NU00676]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00752]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00326]

description: Nanostring SPRINT


title: Stromal, hypodermis, replicate 1

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hypodermis

extract_protocol:
Back skins from C57BL/6 female adult mice were harvested after shaving with an electric clipper. Subcutaneous fat was removed from hypodermis and hypodermal layers were physically isolated from the dermis with forceps. Dermis was isolated from epidermis after 45min of an enzymatic treatment with 0.15% Tripsin/0.75mM EDTA. Isolated dermis and hypodermis were each minced with scissors and digested for 2H at 37°C in RPMI supplemented with 5% FCS and containing 0.25mg/mL of liberase T-Flex and 1ug/mL of DNAse I. Cells were isolated from each layer and immunostained with anti-EpCAM and anti-CD45 antibodies as well as stained with propidium iodide (PI) before being FACS sorted as live leucocytes (PI–, EpCAM–, CD45+) or live stromal cells (PI–, EpCAM–, CD45–). Cells were then washed, counted and resuspended into PBS containing 0.01% bovine serum albumin before being used for single-cell RNA-sequencing.
Library construction was performed in accordance with 10X Genomics protocol (10X Chromium 3' v2 kit).

value: Hypodermis

value: Stromal cells

tag: strain


title: Stromal, dermis, replicate 2

description: 10x Genomics

source_name: Dermis

value: Dermis


title: Human meningioma, Frozen [NU00592]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00338]

description: Nanostring SPRINT


title: Stromal, hypodermis, replicate 2

description: 10x Genomics


title: Human meningioma, Frozen [NU00300]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-19 B2]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-9]

description: Nanostring SPRINT


title: Stromal, dermis, replicate 1

description: 10x Genomics


title: Human meningioma, FFPE [NU00762]

description: Nanostring SPRINT


title: Human meningioma, FFPE [NU00721]

description: Nanostring SPRINT


title: Leukocytes, hypodermis, replicate 2

description: 10x Genomics

value: Leukocytes


title: Leukocytes, hypodermis, replicate 1

description: 10x Genomics


title: Leukocytes, dermis, replicate 2

description: 10x Genomics


title: Human meningioma, FFPE [NU00606]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00392]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00758]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00225]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00214]

description: Nanostring SPRINT


title: CD8 T cells, Young, rep1

city: San Antonio

first: Anna

last: Allue Guardia

state: Texas

address: 8715 Military Dr W

institute: Texas Biomedical Research Institute

data_processing:
Raw sequencing reads were preprocessed using Trim Galore! 0.6.5 to trim the adapters and low-quality sequences. Parameter --stringency 3 was used.
Trimmed reads were mapped to the mouse GRCm39 reference genome using HISAT2 2.2.1 with default parameters.
Read counts for each sample were obtained using featureCounts (Subread package 2.0.3, 15). Parameters -t exon -g gene_id were used.
Differential gene expression analysis was carried out using  DESeq2 1.38.1 with default parameters.
Assembly: GRCm39
Supplementary files format and content: Raw counts

source_name: Lung

extract_protocol:
Single-cell lung suspensions were obtained from LPS, saline, young, or old mice as follows: first, lungs were perfused with 10 ml PBS containing 50 U/ml heparin and placed into 2 ml c-DMEM, DMEM, 500 ml supplemented with filter-sterilized 5 ml 1M HEPES buffer, 10 ml MEM nonessential amino acid solution 100x, 5 ml Penicillin-Streptomycin 100x, 660 µl 2- mercaptoethanol 50 mM, and 45 ml heat-inactivated fetal bovine serum. A single-cell suspension was obtained using enzymatic digestion. Residual erythrocytes were lysed using Gey’s solution (8 mM NH4Cl, 5 mM KHCO3 in water), passed through a 40 µm strainer, and suspended in c-DMEM. Then, 1-2×107 cells were stained for cell sorting: cells were washed in 1x PBS with 5% FBS and incubated in TruStain FcX-Fc Block diluted in 1x PBS with 5% FBS for 15 min at 4°C. Fc block was removed and cells incubated in antibody cocktails (CD45, APC/Cyanine7, clone 104; CD3, FITC, clone 17A2; CD8, Pacific Blue, clone 53-6.7) diluted in 1x PBS with 5% FBS for 20 min at 4°C in the dark. After staining, cells were washed in Flow Sort Buffer (1x PBS, 5%FBS, 10mM HEPES, 35 µg/ml DNAseI, 5mM MgCl2) and passed through a 40 µm strainer. Cells were washed again in Flow Sort Buffer and stained in Propidium Iodide (Biolegend) according to manufacturer’s instructions. Cells were washed in Flow Sort Buffer once more and kept on ice until sorting using a BD FACs AriaIII. After sorting, CD8 T cells were collected into Trizol and frozen at -80°C until RNA extraction. RNA was extracted using the Direct-Zol RNA Microprep kit (Zymo Research) with an in-column DNAse I treatment, and eluted in DNase/RNase-free water, following the manufacturer’s instructions.
The mRNA-seq library was generated following the Smart-seq2 protocol described in Picelli et al. 2014. 0.8-10 ng of RNA were used in a reverse transcription and template-switching reaction using tailed oligo-dT primers, locked nucleic acid (LNA)-containing template-switching oligos (TSOs), and betaine for cDNA synthesis. Resulting ss-cDNA was amplified (12-14 cycles) for ds-cDNA synthesis, followed by the Nextera XT sample preparation protocol to convert cDNA to library. Samples were pooled after enrichment PCR, and 50SR sequencing was conducted using a single lane of Illumina HiSeq 3000.

treatment_protocol: Lipopolysaccharides (LPS) were injected intraperitoneally (20 µg/mouse in BALB/c or 50 µg/mouse in C57BL/6 in 100 µl normal saline) in LPS mice. Saline injections served as control (Young and Old mice). Mice were injected every 24 hours (hr) ± 2 hr for 4 total injections. Experiments were performed 2 hr after the fourth injection.

value: Lung

value: CD8 T cells

value: BALB/c

tag: Sex

value: female

value: 11-12 weeks old


title: CD8 T cells, Young, rep3


title: CD8 T cells, Young, rep4


title: CD8 T cells, Young, rep2


title: CD8 T cells, Old, rep4

value: 18 month old


title: Human meningioma, FFPE [MEN-14]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-13]

description: Nanostring SPRINT


title: CD8 T cells, Old, rep3


title: Human meningioma, Frozen [1431]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1303]

description: Nanostring SPRINT


title: Human meningioma, FFPE [NU00799]

description: Nanostring SPRINT


title: CD8 T cells, Old, rep2


title: CD8 T cells, LPS, rep4

value: LPS


title: CD8 T cells, LPS, rep3


title: CD8 T cells, LPS, rep2


title: Human meningioma, FFPE [NU00397]

description: Nanostring SPRINT

value: meningioma


title: Human meningioma, FFPE [NU00786]

description: Nanostring SPRINT


title: Leukocytes, dermis, replicate 1

description: 10x Genomics


title: Human meningioma, Frozen [NU00251]

description: Nanostring SPRINT


title: CD8 T cells, LPS, rep1


title: Human meningioma, Frozen [NU00239]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00164]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-15]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-10]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1586]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1508]

description: Nanostring SPRINT


title: endometrial biopsy, URS100

city: Parkville

first: Peter

last: Rogers

state: VIC

address: Level 7, University Department, Royal Women's Hospital, Crn Grattan Street and Flemington Rd

department: Department of Obstetrics and Gynaecology

country: Australia

institute: University of Melbourne

description: Sample URS100 from batch 7

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol with Illumina iScan Reader.

data_processing: Data generated by Illumina iScan Reader was processed by Illumina GenomeStudio software. The data was then normalized in R using background normalization and robust spline normalization with the lumi package and batch corrected with ComBat using the sva package.

label: biotin

source_name: Human endometrium

label_protocol: Biotinylated cRNA was prepared using the Ambion Illumina TotalPrep RNA amplification kit.

extract_protocol: Total RNA was extracted from homogenized endometrial tissues using RNA lysis solution (RLT buffer) and RNeasy Plus Mini Kit according to the manufacturer's instructions.

value: Human endometrium

tag: cycle stage

tag: pod

tag: batch

value: batch 7


title: Human meningioma, FFPE [MEN-12]

description: Nanostring SPRINT


title: Human meningioma, FFPE [NU00795]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00166]

description: Nanostring SPRINT


title: CD8 T cells, Old, rep1


title: Human meningioma, FFPE [NU00414]

description: Nanostring SPRINT


title: Human meningioma, FFPE [NU00385]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00137]

description: Nanostring SPRINT


title: Human meningioma, Frozen [NU00240]

description: Nanostring SPRINT


title: endometrial biopsy, URS080

description: Sample URS080 from batch 6.2

value: batch 6.2


title: endometrial biopsy, URS095

description: Sample URS095 from batch 7


title: endometrial biopsy, URS089

description: Sample URS089 from batch 6.2


title: endometrial biopsy, URS086

description: Sample URS086 from batch 6.2


title: endometrial biopsy, URS090

description: Sample URS090 from batch 7


title: endometrial biopsy, URS044

description: Sample URS044 from batch 6.1

value: batch 6.1


title: endometrial biopsy, URS042

description: Sample URS042 from batch 6.1


title: Human meningioma, FFPE [MEN-1]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-2]

description: Nanostring SPRINT


title: Human meningioma, FFPE [MEN-16]

description: Nanostring SPRINT


title: Human meningioma, Frozen [1026]

description: Nanostring SPRINT


title: Human meningioma, FFPE [AM71]

description: Nanostring nCounter


title: Human meningioma, Frozen [1172]

description: Nanostring SPRINT


title: Human meningioma, FFPE [AM70]

description: Nanostring nCounter


title: endometrial biopsy, URS083

description: Sample URS083 from batch 6.2


title: endometrial biopsy, URS068

description: Sample URS068 from batch 6.2


title: endometrial biopsy, URS070

description: Sample URS070 from batch 6.2


title: endometrial biopsy, URS093

description: Sample URS093 from batch 7


title: endometrial biopsy, URS065

description: Sample URS065 from batch 6.2


title: endometrial biopsy, URS108

description: Sample URS108 from batch 7


title: endometrial biopsy, URS078

description: Sample URS078 from batch 6.2


title: endometrial biopsy, URS077

description: Sample URS077 from batch 6.2


title: endometrial biopsy, URS082

description: Sample URS082 from batch 6.2


title: endometrial biopsy, URS061

description: Sample URS061 from batch 7


title: endometrial biopsy, URS063

description: Sample URS063 from batch 6.2


title: Human meningioma, FFPE [AM69]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM68]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM66]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM67]

description: Nanostring nCounter


title: mouse CD8, 30hr, HashTagOligo

city: Seattle

first: Hao

middle: Yuan

last: Kueh

state: WA

address: 3720 15th Ave NE

department: Bioengineering

institute: University of Washington

description:
10x Genomics
HTO

library_source: other

data_processing:
Data was converted to fastq using bcl2fastq.
Cellranger (version 6.0.1, 10x Genomics) was used for transcriptome- (337M reads) and HTO- (161M reads) level unique molecular identifier (UMI) and cell demultiplexing, and for aligning the transcriptome to the GRCm38/mm10 reference genome.
Doublets and cells with > 7.5% mitochondrial reads were removed.
Quality control, pre-processing, dimensionality reduction, and UMAP visualization were done with Monocle3 (v 1.2.9) in R
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: Spleen

extract_protocol:
Following 30 hrs of stimulation, cells were stained with one of six hashtag (HTO) antibodies (1 ug HTO per sample) for 30 min at 4oC. 22k live cells (4k from each pMHC condition + 2k rested cells) were flow sorted using propidium iodide (Alfa Aesar, Cat # J66584).
Single cell library preparation was done with the 10x Genomics platform, loading all 22k cells into a single lane. Libraries were diluted to 2nM using Agilent Tapestation D1000 HS and loaded onto two NextSeq 2000 P2 100-cycle kits using the following conditions: read 1: 28 cycles; index 1: 8 cycles; read 2: 92 cycles.
scRNA-seq + Hash Tag Oligos

value: Spleen

value: CD8+ T cells

value: WT

tag: time

value: 30 hr

value: 5 different pMHC conditions, or rested


title: Ribo footprint KO 3

city: Gießen

first: Andreas

last: Krueger

address: Schubertstr. 81

country: Germany

institute: Justus Liebig University

description:
RF_masterframe.csv
RFadjusted_countmatrix.csv

data_processing:
Total RNA reads were checked for quality using FastqC and adapters were removed using Flexbar (version 3.5.0/adapter sequence: "AGATCGGAAGAGCACACGTCT", options: --min-read-length 15 -ao 1).
rRNA was removed with Bowtie2 (version 2.5.1/options: --very-sensitive -x rRNA)
reads were aligned to the mouse genome (gencode M23) using STAR aligner (version: 2.7.10a /options: --outFilterMultimapNmax 5 --alignEndsType EndToEnd).
Reads per gene were counted using htseq-count (version 2.0.3/options: --stranded=yes) with default settings and GENCODE gene annotation (M23)
Differential expression analysis between miR-181 KO and WT samples was performed using DESeq2 (version 1.40.2)
Assembly: gencode.VM23
Supplementary files format and content: Htseq output as .txt table with gene names and counts
Supplementary files format and content: DEseq2 Output (KO vs WT) as .csv tables
Library strategy: Ribosome profiling

source_name: Thymus

growth_protocol: Mice were grown to 6 weeks of age under SPF conditions.

extract_protocol:
RPF samples were treated and RNA was isolated according to manufacturers instructions using the Illumina TruSeq Ribo Profile (Mammalian) kit.
Libraries were contrsucted using the Illumina TruSeq Ribo Profile (Mammalian) kit.

treatment_protocol: Thymocytes were isolated from mouse thymy using 70µm strainers and were immediately submerged in DPBS containing 0.1mg/ml cycloheximide.

value: Thymus

value: Thymocytes

value: miR-181a/b-1 KO


title: Ribo footprint KO 2


title: mouse CD8, 30hr, Transcriptome

description:
10x Genomics
Transcriptome

molecule: polyA RNA


title: Human meningioma, FFPE [AM65]

description: Nanostring nCounter


title: Ribo footprint KO 1


title: Human meningioma, FFPE [AM64]

description: Nanostring nCounter


title: endometrial biopsy, URS047

description: Sample URS047 from batch 6.1


title: Ribo footprint WT 3


title: endometrial biopsy, URS043

description: Sample URS043 from batch 6.1


title: endometrial biopsy, URS038

description: Sample URS038 from batch 6.1


title: endometrial biopsy, URS049

description: Sample URS049 from batch 6.1


title: endometrial biopsy, URS028

description: Sample URS028 from batch 6.1


title: endometrial biopsy, URS030

description: Sample URS030 from batch 6.1


title: endometrial biopsy, URS027

description: Sample URS027 from batch 6.1


title: Ribo footprint WT 1


title: Human meningioma, FFPE [AM63]

description: Nanostring nCounter


title: endometrial biopsy, URS029

description: Sample URS029 from batch 6.1


title: endometrial biopsy, URS048

description: Sample URS048 from batch 7


title: Human meningioma, FFPE [AM61]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM60]

description: Nanostring nCounter


title: RNAseq KO 2

description:
RNA_masterframe.csv
RNAadjusted_countmatrix.csv

data_processing:
Total RNA reads were checked for quality using FastqC and adapters were removed using Flexbar (version 3.5.0/adapter sequence: "AGATCGGAAGAGCACACGTCT", options: --min-read-length 15 -ao 1).
rRNA was removed with Bowtie2 (version 2.5.1/options: --very-sensitive -x rRNA)
reads were aligned to the mouse genome (gencode M23) using STAR aligner (version: 2.7.10a /options: --outFilterMultimapNmax 5 --alignEndsType EndToEnd).
Reads per gene were counted using htseq-count (version 2.0.3/options: --stranded=yes) with default settings and GENCODE gene annotation (M23)
Differential expression analysis between miR-181 KO and WT samples was performed using DESeq2 (version 1.40.2)
Assembly: gencode.VM23
Supplementary files format and content: Htseq output as .txt table with gene names and counts
Supplementary files format and content: DEseq2 Output (KO vs WT) as .csv tables


title: Human meningioma, FFPE [AM62]

description: Nanostring nCounter


title: endometrial biopsy, URS019

description: Sample URS019 from batch 6.1


title: Ribo footprint WT 2


title: RNAseq KO 1


title: endometrial biopsy, URS115

description: Sample URS115 from batch 7


title: endometrial biopsy, URS008

description: Sample URS008 from batch 6.1


title: endometrial biopsy, URS017

description: Sample URS017 from batch 6.1


title: endometrial biopsy, URS010

description: Sample URS010 from batch 7


title: endometrial biopsy, URS005

description: Sample URS005 from batch 6.1


title: endometrial biopsy, URS113

description: Sample URS113 from batch 7


title: endometrial biopsy, URS114

description: Sample URS114 from batch 7


title: endometrial biopsy, URS021

description: Sample URS021 from batch 6.1


title: endometrial biopsy, URS023

description: Sample URS023 from batch 6.1


title: Human meningioma, FFPE [AM57]

description: Nanostring nCounter


title: RNAseq WT 3


title: Human meningioma, FFPE [AM55]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM56]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM59]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM54]

description: Nanostring nCounter


title: RNAseq WT 2


title: endometrial biopsy, URS097

description: Sample URS097 from batch 7


title: endometrial biopsy, URS107

description: Sample URS107 from batch 7


title: endometrial biopsy, URS111

description: Sample URS111 from batch 7


title: endometrial biopsy, URS088

description: Sample URS088 from batch 6.2


title: Human meningioma, FFPE [AM53]

description: Nanostring nCounter


title: endometrial biopsy, URS099

description: Sample URS099 from batch 7


title: endometrial biopsy, URS091

description: Sample URS091 from batch 7


title: endometrial biopsy, URS112

description: Sample URS112 from batch 7


title: Human meningioma, FFPE [AM51]

description: Nanostring nCounter


title: endometrial biopsy, URS085

description: Sample URS085 from batch 6.2


title: KD3010GL261

city: Houston

first: Ailiang

last: Zeng

state: TX

address: 12515 stoney creek dr

department: Cancer Biology

institute: MD Anderson Cancer Center

description: 10x Genomics

data_processing:
FastQ preparation: mkfastq (cellranger):https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq
Count Matrix Generation: count (cellranger):https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count
Data Normalization: scTransform (Satija):https://satijalab.org/seurat/v3.1/sctransform_vignette.html
https://satijalab.org/seurat/articles/integration_large_datasets.html
Assembly: mm10-3.0.0 (mouse), GRCh38-3.0.0 (human)
Supplementary files format and content: tsv.gz/barcodes
Supplementary files format and content: tsv.gz/genes
Supplementary files format and content: mtx.gz/counts

source_name: glioblatoma

extract_protocol:
Tumor samples were mechanically minced before enzymatic digestion, cells were then spun down at 800g with the brake off in a 0.9M sucrose solution to remove myelin. Cell pellets were then frozen. Upon bringing samples back up CD45+ FACs selection was performed before entering the 10x protocol
https://assets.ctfassets.net/an68im79xiti/4tjk4KvXzTWgTs8f3tvUjq/2259891d68c53693e753e1b45e42de2d/CG000183_ChromiumSingleCell3__v3_UG_Rev_C.pdf

value: glioblatoma

value: immune cells


title: endometrial biopsy, URS087

description: Sample URS087 from batch 6.2


title: Human meningioma, FFPE [AM52]

description: Nanostring nCounter


title: VehicleGL261

description: 10x Genomics

value: Vehicle


title: RNAseq WT 1


title: SpontaneousEarly2

description: 10x Genomics

value: QPP

value: Tamoxifen


title: SpontaneousEarly3

description: 10x Genomics


title: Human meningioma, FFPE [AM50]

description: Nanostring nCounter

value: meningioma


title: endometrial biopsy, URS081

description: Sample URS081 from batch 6.2

value: Human endometrium


title: SpontaneousEarly1

description: 10x Genomics


title: Human meningioma, FFPE [AM49]

description: Nanostring nCounter


title: endometrial biopsy, URS072

description: Sample URS072 from batch 6.2

value: batch 6.2


title: endometrial biopsy, URS076

description: Sample URS076 from batch 6.2


title: endometrial biopsy, URS075

description: Sample URS075 from batch 6.2


title: endometrial biopsy, URS074

description: Sample URS074 from batch 6.2


title: endometrial biopsy, URS069

description: Sample URS069 from batch 6.2


title: endometrial biopsy, URS071

description: Sample URS071 from batch 6.2


title: SpontaneousCtrl3

description: 10x Genomics

source_name: Control

value: Control


title: endometrial biopsy, URS073

description: Sample URS073 from batch 6.2


title: Human meningioma, FFPE [AM48]

description: Nanostring nCounter


title: endometrial biopsy, URS024

description: Sample URS024 from batch 6.1

value: batch 6.1


title: endometrial biopsy, URS067

description: Sample URS067 from batch 6.2


title: Human meningioma, FFPE [AM47]

description: Nanostring nCounter


title: SpontaneousCtrl1

description: 10x Genomics


title: Male3Core

description: 10x Genomics


title: SpontaneousCtrl2

description: 10x Genomics


title: Human meningioma, FFPE [AM45]

description: Nanostring nCounter


title: endometrial biopsy, URS062

description: Sample URS062 from batch 6.2


title: endometrial biopsy, URS066

description: Sample URS066 from batch 6.2


title: Male3Border

description: 10x Genomics


title: endometrial biopsy, URS064

description: Sample URS064 from batch 6.2


title: endometrial biopsy, URS060

description: Sample URS060 from batch 6.2


title: endometrial biopsy, URS059

description: Sample URS059 from batch 6.2


title: endometrial biopsy, URS057

description: Sample URS057 from batch 6.2


title: endometrial biopsy, URS058

description: Sample URS058 from batch 6.2


title: endometrial biopsy, URS056

description: Sample URS056 from batch 6.2


title: Human meningioma, FFPE [AM44]

description: Nanostring nCounter


title: Male2Core

description: 10x Genomics


title: Human meningioma, FFPE [AM46]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM43]

description: Nanostring nCounter


title: Male2Border

description: 10x Genomics


title: endometrial biopsy, URS055

description: Sample URS055 from batch 6.2


title: Male2_3_mix_Periphery

description: 10x Genomics


title: Human meningioma, FFPE [F95]

description: Nanostring nCounter


title: endometrial biopsy, URS054

description: Sample URS054 from batch 6.2


title: Female6Core

description: 10x Genomics


title: Female6Border

description: 10x Genomics


title: Human meningioma, FFPE [F93]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM42]

description: Nanostring nCounter


title: Human meningioma, FFPE [F92]

description: Nanostring nCounter


title: Female6Periphery

description: 10x Genomics


title: endometrial biopsy, URS039

description: Sample URS039 from batch 6.1


title: Female4Border

description: 10x Genomics


title: endometrial biopsy, URS051

description: Sample URS051 from batch 6.1


title: Human meningioma, FFPE [F90]

description: Nanostring nCounter


title: endometrial biopsy, URS033

description: Sample URS033 from batch 6.1


title: endometrial biopsy, URS045

description: Sample URS045 from batch 6.1


title: endometrial biopsy, URS032

description: Sample URS032 from batch 6.1


title: endometrial biopsy, URS041

description: Sample URS041 from batch 6.1


title: endometrial biopsy, URS052

description: Sample URS052 from batch 7

value: batch 7


title: endometrial biopsy, URS036

description: Sample URS036 from batch 6.1


title: endometrial biopsy, URS031

description: Sample URS031 from batch 6.1


title: Human meningioma, FFPE [F94]

description: Nanostring nCounter


title: endometrial biopsy, URS050

description: Sample URS050 from batch 6.1


title: endometrial biopsy, URS037

description: Sample URS037 from batch 6.1


title: endometrial biopsy, URS040

description: Sample URS040 from batch 6.1


title: endometrial biopsy, URS034

description: Sample URS034 from batch 6.1


title: Female4Periphery

description: 10x Genomics


title: endometrial biopsy, URS026

description: Sample URS026 from batch 6.1


title: endometrial biopsy, URS022

description: Sample URS022 from batch 6.1


title: endometrial biopsy, URS020

description: Sample URS020 from batch 6.1


title: Human meningioma, FFPE [F89]

description: Nanostring nCounter


title: endometrial biopsy, URS016

description: Sample URS016 from batch 6.1


title: Female4Core

description: 10x Genomics


title: RNAseq KO 3


title: Human meningioma, FFPE [F88]

description: Nanostring nCounter


title: Female3Core

description: 10x Genomics


title: Human meningioma, FFPE [F91]

description: Nanostring nCounter


title: Female3Border

description: 10x Genomics


title: Human meningioma, FFPE [F87]

description: Nanostring nCounter


title: endometrial biopsy, URS015

description: Sample URS015 from batch 6.1


title: Human meningioma, FFPE [F86]

description: Nanostring nCounter


title: endometrial biopsy, URS012

description: Sample URS012 from batch 6.1


title: Female3Periphery

description: 10x Genomics


title: Human meningioma, FFPE [F83]

description: Nanostring nCounter


title: endometrial biopsy, URS014

description: Sample URS014 from batch 6.1


title: nephron progenitors of Smo WT, replicate 2

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-seq reads were aligned to UCSC mouse genome 10 mm using STAR aligner. Only uniquely aligned reads were used for downstream analysis. Raw read counts for each gene were measured using FeatureCounts in the subread package with an option, “-s 2 -O --fracOverlap 0.8”.
Assembly: mm10
Supplementary files format and content: Tab delimited gene read count file in raw counts and RPKM normalized counts

source_name: kidney

extract_protocol:
Total RNA from FACS isolated cells were prepared using Single Cell RNA Purification Kit (Norgen). From total RNA, mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs) following manufacturer’s instructions. Fragmentation of RNA followed by reverse transcription and second strand cDNA synthesis was done using NEBNext RNA First Strand Synthesis Module (E7525L) and NEBNext RNA Second Strand Synthesis Module (E6111L) following manufacturer’s instructions.
The resulting double-stranded cDNA’s were further processed to DNA sequencing libraries using ThruPLEX DNA-seq 12S Kit (R400428, Clontech Laboratories). Libraries were size-selected by gel purification for an average size of 350bp.

value: kidney

value: Smo +/+ ; Six2GFPcre

value: FACS-isolated mesenchymal nephron progenitors


title: Human meningioma, FFPE [F82]

description: Nanostring nCounter


title: nephron progenitors of SmoM2 Transgenic, replicate 1

value: Rosa26 SmoM2/+ ;Smo +/+ ; Six2GFPcre


title: endometrial biopsy, URS018

description: Sample URS018 from batch 6.1


title: Human meningioma, FFPE [F81]

description: Nanostring nCounter


title: nephron progenitors of Smo WT, replicate 1


title: endometrial biopsy, URS011

description: Sample URS011 from batch 6.1


title: endometrial biopsy, URS007

description: Sample URS007 from batch 6.1


title: endometrial biopsy, URS001

description: Sample URS001 from batch 6.1


title: endometrial biopsy, X210043

description: Sample X210043 from batch 1

value: batch 1


title: nephron progenitors of Smo Het, replicate 2

value: Smo c/+ ; Six2GFPcre


title: endometrial biopsy, X210229

description: Sample X210229 from batch 3

value: batch 3


title: endometrial biopsy, X210474

description: Sample X210474 from batch 7


title: endometrial biopsy, URS003

description: Sample URS003 from batch 7


title: Human meningioma, FFPE [F75]

description: Nanostring nCounter


title: Human meningioma, FFPE [F76]

description: Nanostring nCounter


title: endometrial biopsy, URS004

description: Sample URS004 from batch 6.1


title: nephron progenitors of Smo Het, replicate 1


title: Human meningioma, FFPE [F73]

description: Nanostring nCounter


title: nephron progenitors of Smo KO, replicate 1

value: Smo c/c ; Six2GFPcre


title: nephron progenitors of SmoM2 Transgenic, replicate 2


title: nephron progenitors of Smo KO, replicate 2


title: endometrial biopsy, X210321

description: Sample X210321 from batch 5

value: batch 5


title: endometrial biopsy, URS009

description: Sample URS009 from batch 6.1


title: Human meningioma, FFPE [F77]

description: Nanostring nCounter


title: endometrial biopsy, X210184

description: Sample X210184 from batch 3


title: Human meningioma, FFPE [F72]

description: Nanostring nCounter


title: endometrial biopsy, X210287

description: Sample X210287 from batch 5


title: endometrial biopsy, X210506

description: Sample X210506 from batch 7


title: endometrial biopsy, X210111

description: Sample X210111 from batch 2

value: batch 2


title: endometrial biopsy, X210417

description: Sample X210417 from batch 7


title: endometrial biopsy, X210151

description: Sample X210151 from batch 2


title: endometrial biopsy, X210027

description: Sample X210027 from batch 1


title: Avil-ChR2 mouse#40

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

institute: Goethe University Frankfurt

data_processing:
Sample quality was assessed with demultiplexed fastq.gz files and subsequently the alignment was performed with SeqMan NGen 17 (Lasergene) using the reference genome mm10 provided from UCSC (GRCm38) as template, a minimum read length of 35 bp and automatic adapter trimming.
Results were displayed with ArrayStar 17 (Lasergene) including the amount of mapped reads, target length, source length and position, strand, genes and gene IDs, annotated according to the mm10 assembly. The reads were normalized according to EdgeR.
Normalized reads were analyzed with ArrayStar 17, which uses general linear models to assess differential expression.
Genes were filtered for at least 12 valid values (EdgeR log2 > -5) out of 16 samples to exclude low expression genes.
Assembly: mm10
Supplementary files format and content: ELP_EdgeR_36930_allgenes.txt (tab delimited txt file with EdgeR normalized counts for each biological replicate i.e. mouse )
ELPassembly_EdgeR_Valid21695.txt (tab delimited txt file with EdgeR normalized counts of the biological replicates, i.e. mice of filtered valid genes)

source_name: Brain Cortex

growth_protocol: does not apply

extract_protocol:
Cortices were removed, flash frozen on dry ice, and total RNA was extracted using Qiagen RNeasy spin columns. Illumina TruSeq mRNA Sample Prep Kit was used with 1 µg of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina's instructions.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Mice were exposed to blue light in a chamber from postnatal day p1 to p5, once daily for 1h. Tissue was dissected on p7.

value: Cortex

value: 7 days

tag: gender

value: female

value: Advillin-ChR2 positive

value: blue light


title: endometrial biopsy, X210510

description: Sample X210510 from batch 7

value: Human endometrium


title: Human meningioma, FFPE [F71]

description: Nanostring nCounter

value: meningioma


title: Avil-ChR2 mouse#39

value: male


title: Human meningioma, FFPE [F70]

description: Nanostring nCounter


title: endometrial biopsy, X210491

description: Sample X210491 from batch 7

value: batch 7


title: Avil-ChR2 mouse#38


title: Human meningioma, FFPE [F69]

description: Nanostring nCounter


title: Avil-ChR2 mouse#37


title: Avil-ChR2 mouse#31


title: endometrial biopsy, X210244

description: Sample X210244 from batch 3


title: endometrial biopsy, X210201

description: Sample X210201 from batch 3


title: Human meningioma, FFPE [F67]

description: Nanostring nCounter


title: endometrial biopsy, X210003

description: Sample X210003 from batch 1


title: Human meningioma, FFPE [F66]

description: Nanostring nCounter


title: Avil-ChR2 mouse#30


title: endometrial biopsy, X210369

description: Sample X210369 from batch 6.2

value: batch 6.2


title: endometrial biopsy, X210132

description: Sample X210132 from batch 2


title: Avil-ChR2 mouse#29


title: endometrial biopsy, X210217

description: Sample X210217 from batch 3


title: endometrial biopsy, X210380

description: Sample X210380 from batch 5


title: Human meningioma, FFPE [F64]

description: Nanostring nCounter


title: endometrial biopsy, X210281

description: Sample X210281 from batch 5


title: Human meningioma, FFPE [F63]

description: Nanostring nCounter


title: Avil-ChR2 mouse#28


title: endometrial biopsy, X210228

description: Sample X210228 from batch 3


title: ChR2-flfl mouse #41

value: ChR2-flfl floxed control


title: Human meningioma, FFPE [F62]

description: Nanostring nCounter


title: Human meningioma, FFPE [F61]

description: Nanostring nCounter


title: endometrial biopsy, X210325

description: Sample X210325 from batch 5


title: endometrial biopsy, X210395

description: Sample X210395 from batch 5


title: endometrial biopsy, X210428

description: Sample X210428 from batch 7


title: endometrial biopsy, X210322

description: Sample X210322 from batch 5


title: endometrial biopsy, X210527

description: Sample X210527 from batch 7


title: endometrial biopsy, X210128

description: Sample X210128 from batch 2


title: endometrial biopsy, X210505

description: Sample X210505 from batch 7


title: endometrial biopsy, X210140

description: Sample X210140 from batch 2


title: ChR2-flfl mouse #36


title: Human meningioma, FFPE [F65]

description: Nanostring nCounter


title: endometrial biopsy, X210087

description: Sample X210087 from batch 1

value: batch 1


title: Human meningioma, FFPE [F59]

description: Nanostring nCounter


title: ChR2-flfl mouse #33


title: ChR2-flfl mouse #35


title: ChR2-flfl mouse #42


title: endometrial biopsy, X210202

description: Sample X210202 from batch 3


title: endometrial biopsy, X210435

description: Sample X210435 from batch 7


title: endometrial biopsy, X210543

description: Sample X210543 from batch 7


title: Human meningioma, FFPE [F56]

description: Nanostring nCounter


title: ChR2-flfl mouse #32


title: endometrial biopsy, X210149

description: Sample X210149 from batch 2


title: endometrial biopsy, X210105

description: Sample X210105 from batch 2


title: endometrial biopsy, X210341

description: Sample X210341 from batch 5


title: endometrial biopsy, X210367

description: Sample X210367 from batch 5


title: endometrial biopsy, X210059

description: Sample X210059 from batch 1


title: Human meningioma, FFPE [F55]

description: Nanostring nCounter


title: Human meningioma, FFPE [F53]

description: Nanostring nCounter


title: ChR2-flfl mouse #27


title: Human meningioma, FFPE [F54]

description: Nanostring nCounter


title: Human meningioma, FFPE [F57]

description: Nanostring nCounter


title: endometrial biopsy, X210382

description: Sample X210382 from batch 5


title: Human meningioma, FFPE [F52]

description: Nanostring nCounter


title: Pooled input

city: Seoul

first: Soo Yeon

last: Lee

address: yonsei-ro 50-1

country: South Korea

institute: Yonsei university

library_source: genomic

data_processing:
The 75-nt single-end sequence reads generated by Illumina NextSeq 500 are mapped to the genome using the BWA algorithm with default settings. Only reads that pass Illumin’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads are removed.
Since the 5´-ends of the tags represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´- ends to a length of 150-250 bp, depending on the average fragment length in the size selected library. To identify the density of fragments along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
Peak calling was performed with MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Files witt extension*.bw. Binary files that can be opened in or uploaded to genome  browsers and show the fragment density for 32-nt bins along the genome (“signal map”).

molecule: genomic DNA

source_name: Lung sample

growth_protocol: The mice were housed in a specific pathogen-free animal facility, with a controlled temperature and humidity under conditions of a 12-h light/12-h dark cycle.

extract_protocol:
After 2 weeks of PBS or bleomycin treatment, lung samples were harvested and sent to Active Motif for ChIP-sequencing.
Libraries were prepared by Active Motif (Carlsbad, CA) for sequencing using standard Illumina protocols

treatment_protocol: 8-week-old mice were treated PBS or 4mg/kg bleomycin intratracheally.

value: Lung cells

tag: chip antibody


title: ChR2-flfl mouse #26


title: Human meningioma, FFPE [F51]

description: Nanostring nCounter


title: Human meningioma, FFPE [F49]

description: Nanostring nCounter


title: endometrial biopsy, X210102

description: Sample X210102 from batch 2


title: Control_p300-SC

value: PBS


title: endometrial biopsy, X210536

description: Sample X210536 from batch 7


title: endometrial biopsy, X210226

description: Sample X210226 from batch 3

value: batch 3


title: endometrial biopsy, X210114

description: Sample X210114 from batch 2


title: BLM_p300-SC

value: Bleomycin


title: Human meningioma, FFPE [F48]

description: Nanostring nCounter


title: endometrial biopsy, X210152

description: Sample X210152 from batch 2

value: batch 2


title: Pooled MDS M3, Normals N6 N7, cultured 6d, surface protein

first: Christopher

last: Lausted

address: 401 Terry Ave N

institute: ISB

description:
Antibody-derived oligo library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ADT barcode counts) was performed using the 10x Genomics Cell Ranger pipeline with default settings (v3.0) and aligning to the GRCh38 genome build.
Bam files produced by Cell Ranger were analyzed by Velocyto for transcript splice quantification.
Veloctyo transcriptomic results were aggregated by ScanPy (concatenate function). Transcript counts were normalized to 1×10^4 UMIs per cell and log-transformed (log1p function). The aggregated data was saved to a single HDF5 file.
Assembly: GRCh38
Supplementary files format and content: Scanpy HDF5 format: heme_velo_aggr_5exp_211012.h5ad
Library strategy: CITEseq/TotalSeq

source_name: Bone Marrow

growth_protocol: Cryo-preserved bone marrow mononuclear cells were thawed, resuspended in equivalent volume of FBS, washed in HBSS, then resuspended at 1×10^7 cells per ml in PBS, 0.1% BSA, and 2 mM EDTA, and incubated with 1:10 dilution of biotinylated anti-CD3, anti-CD19, and anti-CD11b. Antibody-bound lineage-positive cells were depleted with streptavidin beads. Lineage-depleted marrow mononuclear cells were cultured in erythroid expansion media (IMDM, 5% pooled Human AB plasma, 330 μg/ml holo-transferrin, 1 μM dexamethasone, 160 mM monothioglycerol, 10 μg/ml Insulin, 2 U/ml preservative-free heparin, 2 U/ml EPO, 100 ng/ml SCF and 5 ng/ml IL3) at 2×105 cells/ml. The cells were re-seeded at 2×10^5 cells/ml on day 3 with fresh media.

extract_protocol:
Cells were collected on days 0, 3, and 6.  Cells were washed and resuspended in PBS with 1% BSA at 5×10^5 per ml.  Cells were incubated with 10 μg/ml of each DNA-labelled antibody.
Single-cell mRNA barcoding and library preparation were performed on the 10x Chromium controller according to the manufacturer’s instructions. A single GEM (gel beads-in-emulsion) well from each sample was used to generate both the gene expression and antibody capture libraries which were recombined for sequencing. The libraries were sequenced on Illumina NextSeq 550 or NovaSeq instruments
CITE-seq library preparation was performed according to the Biolegend Totalseq protocol.  (Biolegend TotaSeq or equivalent): CD3, CD11b, CD14, CD36, CD70, CD71/TfR, CD117/cKit, CD235a/GlyA.
Following the final bead purification, all three libraries were pooled as 85% mRNA library, 10% ADT library and 5% PhiX Control library before sequencing.

value: Bone Marrow

value: Bone marrow mononuclear cells (BMMC)

tag: disease state

value: Myelodysplastic Syndrome and normal

tag: library type

value: ADT

tag: antibodies/tags

value: Anti-CD3, CD11b, CD14, CD36, CD70, CD71/TfR, CD117/cKit, CD235a/GlyA.


title: endometrial biopsy, X210450

description: Sample X210450 from batch 7

value: Human endometrium


title: endometrial biopsy, X210345

description: Sample X210345 from batch 5

value: batch 5


title: endometrial biopsy, X210432

description: Sample X210432 from batch 7


title: endometrial biopsy, X210499

description: Sample X210499 from batch 7


title: endometrial biopsy, X210156

description: Sample X210156 from batch 2


title: Human meningioma, FFPE [F47]

description: Nanostring nCounter

tag: disease

value: meningioma


title: Bovine satellite cells, differentiation timecourse

city: Maastricht

first: Tobias

last: Messmer

address: Watermolen 28

department: Cell Biology

country: Netherlands

institute: Mosa Meat

description: 10x Genomics

data_processing:
Demultiplexed FASTQ files were generated from BCL files using the mkfastq function  (CellRanger 6.01).
Using CellRanger’s count function, sequencing reads were mapped to the Bos Taurus genome (build ARS-UCD1.2), annotated (Ensembl release 101) and filtered with default parameters. All reads, including those mapping to introns, were used for subsequent analysis.
The gene expression matrix was obtained by applying default filtering parameters of CellRanger. The previously generated VCF files were used to assign genotype-probabilities to each barcode using demuxlet.
In total, we identified 18021 nuclei, of which 4999 were unambiguously categorised as singlets (attached processed data file). Low-quality nuclei (three median absolute deviations above the median of expressed genes, total counts or percentage mitochondrial genes) were removed, leaving 4618 nuclei for downstream analysis
Assembly: bosTau9
Supplementary files format and content: barcodes.tsv.gz contains all UMIs.
Supplementary files format and content: features.tsv.gz contains gene information.
Supplementary files format and content: matrix.mtx.gz contains raw counts derived from CellRanger.
Supplementary files format and content: meta_data.tsv contains meta information for each UMI including genotype information.

molecule: nuclear RNA

organism: Bos taurus

source_name: satellite cells

growth_protocol: Satellite cells (SCs) were proliferated in SFGM on laminin-521 (0.5 μg cm-2, LN521-05, Biolamina) coated tissue culture vessels.

extract_protocol:
On the day of harvest, nuclei were harvested by adapting a previously published protocol. Cells were kept on an ice-cooled platform, washed with 1% BSA + 0.25 M Sucrose and lysed with 2.5% Triton-X100 for 10 min. The lysate was collected using a cell scraper, diluted with 1 % BSA + 0.25 M Sucrose, filtered with a 100 µm strainer and centrifuged to a crude pellet (3000 × g, 10 min). Nuclei pellets for each genotype were resuspended in Injection-buffer (1% BSA/RNase-free PBS + RNAse inhibitor), filtered with a 40 µm filter and quantified using a Countess 3 cell counter (Thermo Fisher) prior to injection.
Quantified nuclei from all timepoints were mixed in an equal ratio. 25 000 total nuclei from this mixture were emulsified in barcoded gel beads using a Chromium Single Cell Controller (10x Genomics). NextGEM Single Cell 3’ Kit V3.1 (10x Genomics) was used for library preparation. A Novaseq 6000 system (Illumina) with a NovaSeq S1 flow-cell was used for paired-end 3’ sequencing of cDNA reads until a total depth of 3.5x108 was achieved.

treatment_protocol: To study the nuclear transcriptomic hetereogeneity during differentiation, SCs from two different animals were seeded at 5E4/cm^2 on subsequent days and differentiated in SFDM on 0.5% Matrigel coated cell culture vessels for 96 h, 72 h, 48 h, 24 h or 0 h, resulting in a total of 10 samples with unique genotypes.

value: satellite cells

tag: time point

value: multiplexed sample:0 h, 24 h, 48 h, 72 h, 96 h


title: Pooled MDS M3, Normals N6 N7, cultured 3d, surface protein

tag: tissue

tag: cell type


title: Human meningioma, FFPE [F46]

description: Nanostring nCounter


title: endometrial biopsy, X210447

description: Sample X210447 from batch 7

tag: age

value: batch 7


title: endometrial biopsy, X210347

description: Sample X210347 from batch 5


title: Pooled MDS M3, Normals N6 N7, uncultured, surface protein


title: Human meningioma, FFPE [F45]

description: Nanostring nCounter


title: Pooled MDS M3, Normals N6 N7, cultured 6d, mRNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
polyA RNA

value: mRNA


title: endometrial biopsy, X210311

description: Sample X210311 from batch 5


title: Pooled MDS M3, Normals N6 N7, cultured 3d, mRNA


title: Human meningioma, FFPE [F44]

description: Nanostring nCounter


title: endometrial biopsy, X210339

description: Sample X210339 from batch 6.2

value: batch 6.2


title: endometrial biopsy, X210329

description: Sample X210329 from batch 5


title: endometrial biopsy, X210224

description: Sample X210224 from batch 3


title: endometrial biopsy, X210083

description: Sample X210083 from batch 1

value: batch 1


title: endometrial biopsy, X210125

description: Sample X210125 from batch 2


title: endometrial biopsy, X210141

description: Sample X210141 from batch 2


title: endometrial biopsy, X210358

description: Sample X210358 from batch 5


title: Pooled MDS M3, Normals N6 N7, uncultured, mRNA


title: Human meningioma, FFPE [F40]

description: Nanostring nCounter


title: Pooled MDS M2, Normals N6 N7, cultured 3d, surface protein


title: Human meningioma, FFPE [F39]

description: Nanostring nCounter


title: Human meningioma, FFPE [F38]

description: Nanostring nCounter


title: Pooled MDS M2, Normals N6 N7, uncultured, surface protein


title: Human meningioma, FFPE [F43]

description: Nanostring nCounter


title: Human meningioma, FFPE [F37]

description: Nanostring nCounter


title: Pooled MDS M2, Normals N6 N7, cultured 6d, mRNA


title: Human meningioma, FFPE [F42]

description: Nanostring nCounter


title: Pooled MDS M2, Normals N6 N7, cultured 6d, surface protein


title: endometrial biopsy, X210381

description: Sample X210381 from batch 6.2


title: Human meningioma, FFPE [F36]

description: Nanostring nCounter


title: Pooled MDS M2, Normals N6 N7, uncultured, mRNA


title: Pooled MDS M2, Normals N6 N7, cultured 3d, mRNA


title: endometrial biopsy, X210335

description: Sample X210335 from batch 5


title: endometrial biopsy, X210241

description: Sample X210241 from batch 3

value: batch 3


title: endometrial biopsy, X210423

description: Sample X210423 from batch 7


title: endometrial biopsy, X210424

description: Sample X210424 from batch 7


title: endometrial biopsy, X210182

description: Sample X210182 from batch 3


title: Human meningioma, FFPE [F35]

description: Nanostring nCounter


title: endometrial biopsy, X210373

description: Sample X210373 from batch 5


title: endometrial biopsy, X210055

description: Sample X210055 from batch 1


title: endometrial biopsy, X210108

description: Sample X210108 from batch 2


title: endometrial biopsy, X210532

description: Sample X210532 from batch 7


title: endometrial biopsy, X210185

description: Sample X210185 from batch 3


title: Pooled MDS M1, Normal N5, cultured0/3/6d, surface protein


title: endometrial biopsy, X210507

description: Sample X210507 from batch 7


title: Human meningioma, FFPE [F34]

description: Nanostring nCounter


title: endometrial biopsy, X210516

description: Sample X210516 from batch 7


title: endometrial biopsy, X210473

description: Sample X210473 from batch 7


title: endometrial biopsy, X210538

description: Sample X210538 from batch 7


title: endometrial biopsy, X210464

description: Sample X210464 from batch 7


title: Human meningioma, FFPE [F33]

description: Nanostring nCounter


title: endometrial biopsy, X210388

description: Sample X210388 from batch 5


title: Pooled MDS M1, Normal N5, cultured 6d, mRNA


title: Pooled MDS M1, Normal N5, cultured 3d, mRNA


title: Human meningioma, FFPE [F32]

description: Nanostring nCounter


title: Pooled MDS M1, Normal N5, uncultured, mRNA


title: endometrial biopsy, X210091

description: Sample X210091 from batch 1


title: Pooled DBA D1, Normal N4, cultured0/3/6d, surface protein

value: Diamond-Blackfan Anemia and normal


title: Human meningioma, FFPE [F29]

description: Nanostring nCounter


title: endometrial biopsy, X210533

description: Sample X210533 from batch 7


title: endometrial biopsy, X210045

description: Sample X210045 from batch 1


title: endometrial biopsy, X210501

description: Sample X210501 from batch 7


title: endometrial biopsy, X210309

description: Sample X210309 from batch 5


title: endometrial biopsy, X210051

description: Sample X210051 from batch 1


title: endometrial biopsy, X210061

description: Sample X210061 from batch 1


title: Pooled DBA D1, Normal N4, cultured 6d, mRNA


title: Human meningioma, FFPE [F28]

description: Nanostring nCounter


title: Human meningioma, FFPE [F30]

description: Nanostring nCounter


title: endometrial biopsy, X210221

description: Sample X210221 from batch 3


title: endometrial biopsy, X210462

description: Sample X210462 from batch 7


title: endometrial biopsy, X210504

description: Sample X210504 from batch 7


title: Pooled DBA D1, Normal N4, cultured 3d, mRNA


title: Pooled DBA D1, Normal N4, uncultured, mRNA


title: Human meningioma, FFPE [F27]

description: Nanostring nCounter


title: endometrial biopsy, X210298

description: Sample X210298 from batch 6.2


title: endometrial biopsy, X210476

description: Sample X210476 from batch 7


title: Pooled DBA D1 D2, Normal N1 N3, cultured 6d, surface protein


title: Human meningioma, FFPE [F24]

description: Nanostring nCounter


title: endometrial biopsy, X210190

description: Sample X210190 from batch 3


title: Pooled DBA D1 D2, Normal N1 N3, cultured 3d, surface protein


title: Human meningioma, FFPE [F23]

description: Nanostring nCounter


title: Human meningioma, FFPE [F22]

description: Nanostring nCounter


title: endometrial biopsy, X210028

description: Sample X210028 from batch 1


title: endometrial biopsy, X210000

description: Sample X210000 from batch 1


title: Human meningioma, FFPE [F26]

description: Nanostring nCounter


title: Pooled DBA D1 D2, Normal N1 N3, uncultured, surface protein


title: Human meningioma, FFPE [F21]

description: Nanostring nCounter


title: Normal N3, cultured 6d, mRNA

value: normal


title: Human meningioma, FFPE [F20]

description: Nanostring nCounter


title: Normal N3, cultured 3d, mRNA

value: Bone Marrow


title: Normal N3, uncultured, mRNA

value: Bone marrow mononuclear cells (BMMC)


title: endometrial biopsy, X210189

description: Sample X210189 from batch 3


title: endometrial biopsy, X210456

description: Sample X210456 from batch 7


title: Human meningioma, FFPE [F19]

description: Nanostring nCounter


title: endometrial biopsy, X210554

description: Sample X210554 from batch 7


title: endometrial biopsy, X210074

description: Sample X210074 from batch 1


title: endometrial biopsy, X210434

description: Sample X210434 from batch 7


title: Human meningioma, FFPE [F18]

description: Nanostring nCounter


title: Normal N2, cultured 6d, mRNA


title: endometrial biopsy, X210468

description: Sample X210468 from batch 7


title: endometrial biopsy, X210365

description: Sample X210365 from batch 5


title: endometrial biopsy, X210375

description: Sample X210375 from batch 6.2


title: endometrial biopsy, X210216

description: Sample X210216 from batch 3


title: endometrial biopsy, X210070

description: Sample X210070 from batch 1


title: endometrial biopsy, X210522

description: Sample X210522 from batch 7


title: endometrial biopsy, X210096

description: Sample X210096 from batch 1


title: endometrial biopsy, X210258

description: Sample X210258 from batch 7


title: endometrial biopsy, X210544

description: Sample X210544 from batch 7


title: endometrial biopsy, X210534

description: Sample X210534 from batch 7


title: Normal N2, uncultured, mRNA


title: Human meningioma, FFPE [F17]

description: Nanostring nCounter


title: Normal N1, cultured 6d, mRNA


title: Human meningioma, FFPE [F15]

description: Nanostring nCounter


title: Normal N1, cultured 3d, mRNA


title: endometrial biopsy, X210525

description: Sample X210525 from batch 7


title: endometrial biopsy, X210304

description: Sample X210304 from batch 5


title: Human meningioma, FFPE [F14]

description: Nanostring nCounter


title: endometrial biopsy, X210494

description: Sample X210494 from batch 7


title: Normal N1, uncultured, mRNA


title: endometrial biopsy, X210399

description: Sample X210399 from batch 6.2


title: Human meningioma, FFPE [F12]

description: Nanostring nCounter


title: endometrial biopsy, X210047

description: Sample X210047 from batch 1


title: Human meningioma, FFPE [F11]

description: Nanostring nCounter


title: endometrial biopsy, X210547

description: Sample X210547 from batch 7


title: endometrial biopsy, X210018

description: Sample X210018 from batch 1


title: DBA D2, cultured 3d, mRNA

value: Diamond-Blackfan Anemia


title: DBA D2, uncultured, mRNA


title: DBA D1, cultured 6d, mRNA


title: Human meningioma, FFPE [F10]

description: Nanostring nCounter


title: Human meningioma, FFPE [F16]

description: Nanostring nCounter


title: DBA D1, cultured 3d, mRNA


title: Human meningioma, FFPE [F7]

description: Nanostring nCounter


title: DBA D2, cultured 6d, mRNA


title: DBA D1, uncultured, mRNA


title: endometrial biopsy, X210126

description: Sample X210126 from batch 2

value: batch 2


title: Human meningioma, FFPE [F6]

description: Nanostring nCounter


title: endometrial biopsy, X210165

description: Sample X210165 from batch 2


title: endometrial biopsy, X210240

description: Sample X210240 from batch 3


title: endometrial biopsy, X210530

description: Sample X210530 from batch 7


title: Human meningioma, FFPE [F5]

description: Nanostring nCounter


title: endometrial biopsy, X210470

description: Sample X210470 from batch 7


title: endometrial biopsy, X210075

description: Sample X210075 from batch 1


title: endometrial biopsy, X210396

description: Sample X210396 from batch 5


title: MDM-IL4 [N2139]

city: Hannover

first: Stephan

last: Immenschuh

state: Deutschland

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine and Transplant Engineering

institute: Hannover Medical School

data_processing:
Raw data were processed by use of nfcore/rRNAseq (version 1.3).
Differential expression analysis and was  conducted  with  DESeq2 (version  1.28.1) in  R.
Genes  with  a  sum  of  reads  of  below  10 across  all  the  samples  were  filtered  out  before  DEGs analysis (significance  threshold  0.05 after Benjamini-Hochberg multiple testing corrections).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Raw counts.csv

source_name: Peripheral blood monocyte-derived macrophages IL-4 polarized

extract_protocol:
The  RNeasy  Plus  Mini  Kit (QIAGEN,  Hilden,  Germany)  was  used  to  isolate  RNA  and remove  genomic  DNA.  RNA  quality  was  assessed  with  the  2100  Bioanalyzer (Agilent Technologies,  Waldbronn,  Germany).  Samples  with  an  RNA  integrity  number (RIN) lower than  7  were  discarded.
The PlM  from  3  healthy  adolescents  were  used  to  prepare  RNA  for transcriptome analysis. In parallel, MDM-0, and MDM-IL4 were utilized for polyA+ library preparation and for the mRNA-seq approach using a NextSeq550 short-read sequencer.

tag: agent


title: Human meningioma, FFPE [F8]

description: Nanostring nCounter


title: endometrial biopsy, X210526

description: Sample X210526 from batch 7


title: endometrial biopsy, X210242

description: Sample X210242 from batch 7


title: endometrial biopsy, X210549

description: Sample X210549 from batch 7


title: MDM-IL4 [N2138]

value: Peripheral blood monocyte-derived macrophages IL-4 polarized


title: endometrial biopsy, X210512

description: Sample X210512 from batch 7

value: Human endometrium


title: endometrial biopsy, X210393

description: Sample X210393 from batch 6.2


title: MDM-IL4 [N2137]


title: Human meningioma, FFPE [F2]

description: Nanostring nCounter


title: endometrial biopsy, X210540

description: Sample X210540 from batch 7


title: endometrial biopsy, X210331

description: Sample X210331 from batch 5

value: batch 5


title: MDM-0 [N2136]

source_name: Peripheral blood monocyte-derived macrophages natural

value: Control


title: Human meningioma, FFPE [F1]

description: Nanostring nCounter

source_name: Human meningioma, FFPE

value: meningioma


title: Human meningioma, FFPE [F3]

description: Nanostring nCounter


title: plMo/Mφ [N1877_N1901]

source_name: Pleural  macrophages

value: Pleural  macrophages


title: endometrial biopsy, X210251

description: Sample X210251 from batch 3


title: Human meningioma, FFPE [AM41]

description: Nanostring nCounter


title: endometrial biopsy, X210255

description: Sample X210255 from batch 5


title: endometrial biopsy, X210219

description: Sample X210219 from batch 3


title: endometrial biopsy, X210167

description: Sample X210167 from batch 2


title: endometrial biopsy, X210492

description: Sample X210492 from batch 7

value: batch 7


title: Human meningioma, FFPE [AM40]

description: Nanostring nCounter


title: MDM-0 [N1876_N1900]

value: Peripheral blood monocyte-derived macrophages natural


title: endometrial biopsy, X210183

description: Sample X210183 from batch 3


title: endometrial biopsy, X210066

description: Sample X210066 from batch 1


title: endometrial biopsy, X210164

description: Sample X210164 from batch 2


title: Human meningioma, FFPE [AM39]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM38]

description: Nanostring nCounter


title: MDM-0 [N1875_N1899]


title: plMo/Mφ [N1874_N1898]


title: MDM-0 [N1873_N1897]


title: Human meningioma, FFPE [AM37]

description: Nanostring nCounter


title: endometrial biopsy, X210550

description: Sample X210550 from batch 7


title: endometrial biopsy, X210415

description: Sample X210415 from batch 7


title: plMo/Mφ [N1872_N1896]


title: endometrial biopsy, X210267

description: Sample X210267 from batch 6.2

value: batch 6.2


title: endometrial biopsy, X210289

description: Sample X210289 from batch 5


title: Human meningioma, FFPE [AM35]

description: Nanostring nCounter


title: endometrial biopsy, X210252

description: Sample X210252 from batch 3


title: endometrial biopsy, X210180

description: Sample X210180 from batch 2


title: endometrial biopsy, X210092

description: Sample X210092 from batch 1

value: batch 1


title: endometrial biopsy, X210256

description: Sample X210256 from batch 5


title: GBM4Core

description: 10x Genomics

value: glioblatoma

value: immune cells

tag: genotype

value: BRCA1, CUL3, DICER1, EGFR, NF1, PIK3R3, RAF1, TERT

tag: treatment


title: endometrial biopsy, X210154

description: Sample X210154 from batch 2

tag: cycle stage


title: endometrial biopsy, X210416

description: Sample X210416 from batch 7

tag: pod


title: Human meningioma, FFPE [AM34]

description: Nanostring nCounter


title: GBM4Border

description: 10x Genomics


title: GBM4Periphery

description: 10x Genomics


title: Human meningioma, FFPE [AM33]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM36]

description: Nanostring nCounter


title: endometrial biopsy, X210414

description: Sample X210414 from batch 7

tag: batch


title: GBM3Core

description: 10x Genomics


title: Human meningioma, FFPE [AM32]

description: Nanostring nCounter


title: GBM3Border

description: 10x Genomics


title: endometrial biopsy, X210308

description: Sample X210308 from batch 5


title: endometrial biopsy, X210376

description: Sample X210376 from batch 6.2


title: endometrial biopsy, X210495

description: Sample X210495 from batch 7


title: Human meningioma, FFPE [AM29]

description: Nanostring nCounter


title: endometrial biopsy, X210246

description: Sample X210246 from batch 3

value: batch 3


title: GBM2Core

description: 10x Genomics

value: PTEN, STAG2, TERT, EGFR, MDM4, PIK3C2B


title: endometrial biopsy, X210323

description: Sample X210323 from batch 5


title: endometrial biopsy, X210496

description: Sample X210496 from batch 7


title: endometrial biopsy, X210352

description: Sample X210352 from batch 6.2


title: endometrial biopsy, X210071

description: Sample X210071 from batch 1


title: endometrial biopsy, X210344

description: Sample X210344 from batch 5


title: endometrial biopsy, X210475

description: Sample X210475 from batch 7


title: GBM3Periphery

description: 10x Genomics


title: endometrial biopsy, X210343

description: Sample X210343 from batch 5


title: Human meningioma, FFPE [AM31]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM28]

description: Nanostring nCounter


title: GBM1Core

description: 10x Genomics

value: P53 mutant


title: Human meningioma, FFPE [AM30]

description: Nanostring nCounter


title: GBM2Periphery

description: 10x Genomics


title: Human meningioma, FFPE [AM27]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM26]

description: Nanostring nCounter


title: endometrial biopsy, X210209

description: Sample X210209 from batch 3


title: GBM2Border

description: 10x Genomics


title: GBM1Border

description: 10x Genomics


title: Human meningioma, FFPE [AM25]

description: Nanostring nCounter


title: GBM1Periphery

description: 10x Genomics


title: endometrial biopsy, X210444

description: Sample X210444 from batch 7


title: Human meningioma, FFPE [AM23]

description: Nanostring nCounter


title: endometrial biopsy, X210312

description: Sample X210312 from batch 5


title: endometrial biopsy, X210524

description: Sample X210524 from batch 7


title: endometrial biopsy, X210223

description: Sample X210223 from batch 3


title: endometrial biopsy, X210204

description: Sample X210204 from batch 3


title: endometrial biopsy, X210262

description: Sample X210262 from batch 7


title: Human meningioma, FFPE [AM24]

description: Nanostring nCounter


title: endometrial biopsy, X210431

description: Sample X210431 from batch 7


title: endometrial biopsy, X210052

description: Sample X210052 from batch 1


title: endometrial biopsy, X210498

description: Sample X210498 from batch 7


title: Month 4 organoid library 3

city: Stanford

first: Ragini

last: Phansalkar

address: 291 Campus Drive

institute: Stanford School of Medicine

data_processing:
ran CellRanger v3.0.1 for Month 2 organoid library 1, Month 3 organoid library1, and Month 4 organoid library 1, v 5.0.1 for the rest.
Assembly: GRCh38
Supplementary files format and content: barcode, matrix, gene names files

source_name: Corneal organoid

extract_protocol:
10xgenomics
Illumina library construction

value: Corneal organoid

tag: cell line

value: peripheral blood-derived iPSCs

value: WT

tag: time

value: Month 4


title: Month 4 organoid library 4


title: endometrial biopsy, X210163

description: Sample X210163 from batch 2

value: Human endometrium

value: batch 2


title: endometrial biopsy, X210511

description: Sample X210511 from batch 7


title: endometrial biopsy, X210079

description: Sample X210079 from batch 1


title: Human meningioma, FFPE [AM22]

description: Nanostring nCounter

value: meningioma


title: endometrial biopsy, X210131

description: Sample X210131 from batch 2


title: Month 4 organoid library 2


title: Human meningioma, FFPE [AM21]

description: Nanostring nCounter


title: Month 4 organoid library 1


title: Human meningioma, FFPE [AM20]

description: Nanostring nCounter


title: endometrial biopsy, X210420

description: Sample X210420 from batch 7

value: batch 7


title: Month 3 organoid library 3

value: Month 3


title: Human meningioma, FFPE [AM19]

description: Nanostring nCounter


title: endometrial biopsy, X210487

description: Sample X210487 from batch 7


title: Month 3 organoid library 2


title: endometrial biopsy, X210421

description: Sample X210421 from batch 7


title: endometrial biopsy, X210371

description: Sample X210371 from batch 5

value: batch 5


title: endometrial biopsy, X210370

description: Sample X210370 from batch 5


title: Human meningioma, FFPE [AM17]

description: Nanostring nCounter


title: endometrial biopsy, X210360

description: Sample X210360 from batch 5


title: endometrial biopsy, X210320

description: Sample X210320 from batch 6.2

value: batch 6.2


title: endometrial biopsy, X210313

description: Sample X210313 from batch 5


title: Month 3 organoid library 1


title: endometrial biopsy, X210210

description: Sample X210210 from batch 3


title: Human meningioma, FFPE [AM18]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM15]

description: Nanostring nCounter


title: Month 2 organoid library 2

value: Month 2


title: endometrial biopsy, X210364

description: Sample X210364 from batch 5


title: endometrial biopsy, X210194

description: Sample X210194 from batch 3


title: Human meningioma, FFPE [AM16]

description: Nanostring nCounter


title: Month 2 organoid library 1


title: Month 2 organoid library 3


title: endometrial biopsy, X210170

description: Sample X210170 from batch 2


title: endometrial biopsy, X210013

description: Sample X210013 from batch 1

value: batch 1


title: endometrial biopsy, X210120

description: Sample X210120 from batch 2


title: Month 1 organoid library 2

value: Month 1


title: Human meningioma, FFPE [AM14]

description: Nanostring nCounter


title: endometrial biopsy, X210161

description: Sample X210161 from batch 2


title: endometrial biopsy, X210127

description: Sample X210127 from batch 2


title: Month 1 organoid library 1


title: endometrial biopsy, X210294

description: Sample X210294 from batch 5


title: endometrial biopsy, X210046

description: Sample X210046 from batch 1


title: Human meningioma, FFPE [AM11]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM13]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM9]

description: Nanostring nCounter


title: Human meningioma, FFPE [AM12]

description: Nanostring nCounter


title: endometrial biopsy, X210166

description: Sample X210166 from batch 2


title: endometrial biopsy, X210537

description: Sample X210537 from batch 7


title: endometrial biopsy, X210269

description: Sample X210269 from batch 5


title: Human meningioma, FFPE [AM10]

description: Nanostring nCounter


title: endometrial biopsy, X210546

description: Sample X210546 from batch 7


title: Human meningioma, FFPE [AM8]

description: Nanostring nCounter


title: 2736_P15_input

city: Tokyo

first: Yukiko

last: Gotoh

state: Tokyo

address: 7-3-1 Hongo, Bunkyo-ku

country: Japan

institute: University of Tokyo

description: Non-immunoprecipitated sample (=input) in 16.0 dpc stage of mouse NPCs (FAC-sorted, HMGA2 OE, replicate 1).

data_processing:
Basecalls performed using Illumina CASAVA version 1.4 at GAIIx and Illumina bcl2fastq-1.8.4 at Hiseq2000/Hiseq2500.
Sequenced reads were aligned to the mm9 reference genome using ELAND v2 software (Illumina).
The bigWig file generated by Homer software using makeTagDirectory and makeUCSCfile.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: neural progenitor cells

growth_protocol:
ChIP-seq: Neocortical NSCs were isolated either by fluorescent activated cell sorting (FACS) from mice expressing the NSC marker, Nestin-d4-Venus, or by manual dissection of the ventricular zone of the neocortex.
RNA-seq: Neocortical NSCs were isolated by fluorescent activated cell sorting (FACS) either from mice expressing the NSC marker, Nestin-d4-Venus or from Ring1A-/-;Ring1Bf/f and Ring1A-/-;Ring1B-/-

extract_protocol:
ChIP-seq: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared according to Illumina's instructions accompanying the Truseq ChIP Prep Kit.
RNA-seq: Total RNA was extracted from cell lysates.
RNA libraries were prepared according to Illumina' s instructions accompanying the Truseq RNA Prep Kit.

treatment_protocol: RNA-seq: For Ring1A-/-;Ring1Bf/f and Ring1A-/-;Ring1B-/-, cells were stained with CD133 antibody and highly positive fraction was isolated as neural stem cells.

tag: strain background

value: ICR

tag: genotype/variation

value: HMGA2 overexpression

tag: Stage

value: neural progenitor cells (NPCs)

tag: chip antibody


title: 2736_P12_input

description: Non-immunoprecipitated sample (=input) in 16.0 dpc stage of mouse NPCs (FAC-sorted, control, replicate 1).


title: 18.5_dpc_RNAseq rep1 [Hiseq2000]

description: total RNA in 18.5 dpc stage of mouse NPCs (Nestin-d4Venus-positive).


title: 2736_P12_IP

description: Immunoprecipitated by anti-H3K27trimethylated Histone antibody in 16.0 dpc stage of mouse NPCs (FAC-sorted, control, replicate 1).

value: H3K27me3 (Millipore, 07-449)


title: Ring1A -/-; Ring1B f/f +cre_RNAseq [Hiseq2000]

description: total RNA in 18.5 dpc stage of mouse NPCs (CD133high) deficient for both Ring1A and Ring1B. Ring1A -/-,Ring1B fl/fl mice with Rosa26CreERT2 were subjected to tamoxifen treatment through maternal intraperitoneal injection at 15.5 dpc.

value: deficient for both Ring1A and Ring1B


title: 18.5_dpc_RNAseq rep2 [Hiseq2000]