title: OS-1 Nuclei Isolation

city: Houston

first: Danh

last: Truong

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Data provided for single-cell or single nucleus RNA-Seq is the raw  count matrix HDF5 file from Cell Ranger

source_name: PDX

extract_protocol: Cells or nuclei were extracted from tissue either from a warm dissociation, cold dissociation, or nucleus isolation protocol. Cells or nuclei were flow sorted to enrich for single live cells and single nuclei.

value: PDX

value: OS cell

tag: group

value: Nuclei


title: SUPT5H_Day6_2

status: Public on Jul 21 2023

type: SRA

city: Boston

first: Danya

middle: J

last: Martell-Smart

state: MA

address: 77 Avenue Louis Pasteur

country: USA

institute: Harvard Medical School

description:
RNAseq library
D6_SPT5_3881_S6

library_source: transcriptomic

data_processing:
Alignement with STAR (custom scripts available at https://github.com/churchmanlab)
Read counts of protein coding genes using featureCounts
nSolver Analysis Software used for extracting and normalizing Nanostring direct mRNA levels (RCC files)
Assembly: GRCh38
Supplementary files format and content: *.csv files contain read counts obtained from featureCounts on bam files

molecule: total RNA

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
Qiazol extraction
RNA sequencing library preparation (SMART-Seq v4 )

tag: tissue

value: Bone Marrow

tag: cell type

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

tag: de-identified donor

tag: developmental stage

value: differntiation in culture Day 6

tag: treatment

value: SUPT5H gRNA


title: MTX, Virus, Day 3, Rep 2

city: Memphis

first: Evan

middle: Peter

last: Williams

state: TN

address: 858 Madison Ave

department: Dept. of Microbiology, Immunology, and Biochemistry

institute: University of Tennessee Health Science Center

data_processing:
CLC Genomics Workbench v 22.0
Sequence reads were trimmed  and filter using default parameters in CLC Genomic Workbench
Trimmed and filter sequence reads were mapped to GRCm39/VEEV_TC-83 concatinated genome using default parameters in CLC Genomic Workbench
Read count results were collected in  CLC Genomic Workbench
Read count were normalized and fold change calculated using DESeq2
Assembly: GRCM39 concatinated with VEEV TC-83 lab reference genome
Supplementary files format and content: tab-delimited text files include total counts for each sample
Supplementary files format and content: tab-delimited text files include total counts, TPM, CPM, and RPKM values for each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
Total RNA was isolated using MagMAX  mirVana Total RNA Isolation Kit on a KingFisher Flex instrument
Libraries were constructed using NEB NEBNext Ultra II RNA Kits

value: Brain

tag: brain region

value: motor cortex

tag: timepoint(dpi)

value: Day 3

tag: genotype

value: Infected with VEEV-TC


title: OS-1 Warm Dissociation

description: 10x Genomics

library_source: transcriptomic single cell

tag: cell line

value: Warm


title: 9L_M_1067

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: age

tag: strain


title: MTX, Virus, Day 5, Rep 3

value: Day 5


title: AAVS1_Day8_1

description:
RNAseq library
D8_AAVS1_3875_S11

value: differntiation in culture Day 8

value: AAVS1 gRNA


title: OS-31 Nuclei Isolation

description: 10x Genomics


title: MTX, Virus, Day 3, Rep 1


title: 9L_M_1065


title: OS-31 Warm Dissociation

description: 10x Genomics


title: AAVS1_Day6_3

description:
RNAseq library
D6_AAVS1_3893_S10


title: 9L_M_1064


title: AAVS1_Day6_2

description:
RNAseq library
D6_AAVS1_3881_S2


title: MTX, Virus, Day 1, Rep 4

value: Day 1


title: AAVS1_Day6_1

description:
RNAseq library
D6_AAVS1_3875_S10


title: MDA-SA98-TIS02 Nuclei Isolation

description: 10x Genomics


title: 9L_M_1063


title: MDA-SA98-TIS02

description: 10x Genomics


title: MTX, Virus, Day 1, Rep 3


title: ES-6 Warm Dissociation

description: 10x Genomics

value: ES cell


title: nucleus_untreated_glia

city: London

first: Oliver

last: Ziff

state: London

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
 mRNA sequencing reads were processed using the nf-core/rna-seq v3.8.1 pipeline.  were assessed utilising FastQC, RSeQC, Qualimap, dupRadar, Preseq and MultiQC tools.
Raw reads underwent adaptor trimming with Trim Galore, removal of ribosomal RNA with SortMeRNA, alignment to Ensembl GRCh38.99 human reference genome using splice-aware aligner, STAR v2.6.1 and BAM level quantification with Salmon to enable transcript level counting.
Detailed quality control of raw and aligned reads were assessed utilising FastQC, RSeQC, Qualimap, dupRadar, Preseq and MultiQC tools.
Assembly: Ensembl GRCh38.99
Supplementary files format and content: Salmon quantified gene abundance per sample

molecule: polyA RNA

source_name: glia

growth_protocol: iPSCs were maintained with Essential 8 Medium media (Life Technologies) on Geltrex (Life Technologies) at 37°C and 5% carbon dioxide. iPSCs were passaged when reaching 70% confluency using EDTA (Life Technologies, 0.5 mM). PSC were plated to 100% confluency and then differentiated to a spinal neural precursor fate by a sequential treatment with small molecules, 0-7: 1μM Dorsomorphin (Millipore), 2μM SB431542 (Tocris Bioscience), and 3.3μM CHIR99021 (Miltenyi Biotec), day 7-14: 0.5μM retinoic acid (Sigma) and 1μM Purmorphamine (Sigma), day 14-18: 0.1μM Purmorphamine. After neural conversion and patterning, 0.1μM Compound E (Enzo Life Sciences) was added to promote terminal differentiation into spinal cord motor neurons.

extract_protocol:
iPSNs underwent subcellular fractionation into nuclear and cytoplasmic compartments using the Ambion PARIS kit cell fractionation buffer, following the manufacturer’s general protocol and an 8M urea nuclear lysis buffer (50mM Tris-HCL (pH8), 100mM NaCl, 0.1% SDS, and 1mM DTT).
Paired-end poly(A)+ selected reverse stranded RNA sequencing libraries were prepared from nuclear and cytoplasmic fractions using the NEBNext® Ultra II Directional RNA Library kit for Illumina®, with 500ng of total RNA as input.

treatment_protocol: For VCP inhibitor treatment, at day 24 of motor neuron differentiation, medium was changed to fresh medium containing 1 μM of ML240 (Sigma; SML1071; CAS: 1346527-98-7), or the same percentage of DMSO for 2 h before harvesting.

value: ipsn

value: glia

value: vcp mutant

value: untreated

tag: strandedness

value: reverse

tag: fraction

value: nucleus


title: 9L_M_1062


title: 9L_M_1066


title: MTX, Virus, Day 1, Rep 2


title: MTX, Virus, Day 1, Rep 1


title: SUPT5H_Day4_3

description:
RNAseq library
D4_SPT5_3893_S13

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: differntiation in culture Day 4

value: SUPT5H gRNA


title: 9L_M_1061


title: ES-6 Nuclei Isolation

description: 10x Genomics

value: PDX

value: Nuclei


title: SUPT5H_Day6_1

description:
RNAseq library
D6_SPT5_3875_S14

value: differntiation in culture Day 6


title: SUPT5H_Day4_2

description:
RNAseq library
D4_SPT5_3881_S5


title: 9L_M_106


title: SUPT5H_Day4_1

description:
RNAseq library
D4_SPT5_3875_S13


title: STR, Virus, Day 7, Rep 3

value: Brain

value: striatum

value: Day 7

value: Infected with VEEV-TC


title: nucleus_untreated_ctrl1

value: ipsn

value: wildtype


title: 9L_M_1058


title: 9L_M_1059


title: STR, Virus, Day 7, Rep 2


title: AAVS1_Day4_2

description:
RNAseq library
D4_AAVS1_3881_S1

value: AAVS1 gRNA


title: AAVS1_Day4_3

description:
RNAseq library
D4_AAVS1_3893_S9


title: ES-4 Warm Dissociation

description: 10x Genomics

value: ES cell

value: Warm


title: ES-4 Nuclei Isolation

description: 10x Genomics


title: STR, Virus, Day 7, Rep 1


title: 9L_M_1057


title: ES-4  Cold Dissociation

description: 10x Genomics

value: Cold


title: MTX, Virus, Day 7, Rep 3

value: motor cortex


title: AAVS1_Day4_1

description:
RNAseq library
D4_AAVS1_3875_S9

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: STR, Virus, Day 7, Rep 4


title: SUPT5H_Day2_2

description:
RNAseq library
D2_SPT5_3893_S13

value: differntiation in culture Day 2

value: SUPT5H gRNA


title: ES-1 Warm Dissociation

description: 10x Genomics

value: PDX


title: STR, Virus, Day 6, Rep 4

value: Day 6


title: 9L_M_1055


title: SUPT5H_Day2_1

description:
RNAseq library
D2_SPT5_3881_S5


title: ES-1 Nuclei Isolation

description: 10x Genomics

value: Nuclei


title: STR, Virus, Day 6, Rep 3

value: Brain

value: striatum


title: AAVS1_Day2_2

description:
RNAseq library
D2_AAVS1_3893_S9


title: 9L_M_1054


title: ES-6  Cold Dissociation

description: 10x Genomics


title: 9L_M_1056


title: ES-1 Cold Dissociation Replicate 1

description: 10x Genomics


title: 9L_M_1052


title: 9L_M_1053


title: nucleus_untreated_ctrl4

value: untreated

value: reverse

value: nucleus


title: STR, Virus, Day 5, Rep 4

value: Day 5

value: Infected with VEEV-TC


title: AAVS1_Day2_1

description:
RNAseq library
D2_AAVS1_3881_S1

value: AAVS1 gRNA


title: ES-1 Cold Dissociation Replicate 2

description: 10x Genomics

value: ES cell

value: Cold


title: STR, Virus, Day 5, Rep 3


title: DSRCT-2 Warm Dissociation

description: 10x Genomics

value: DSRCT cell

value: Warm


title: SUPT5H_Day10_2

description:
RNAseq library
D10_SPT5_3881_S8

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: differntiation in culture Day 10


title: DSRCT-2 Cold Dissociation Replicate 2

description: 10x Genomics

value: PDX


title: 9L_M_1050


title: STR, Virus, Day 5, Rep 2


title: SUPT5H_Day10_1

description:
RNAseq library
D10_SPT5_3875_S16

value: SUPT5H gRNA


title: STR, Virus, Day 6, Rep 2

value: Brain

value: Day 6


title: 9L_M_1051


title: DSRCT-2 Nuclei Isolation

description: 10x Genomics

value: Nuclei


title: 9L_M_105


title: STR, Virus, Day 5, Rep 1

value: striatum


title: AAVS1_Day10_3

description:
RNAseq library
D10_AAVS1_3893_S12


title: STR, Virus, Day 6, Rep 1


title: SUPT5H_Day10_3

description:
RNAseq library
D10_SPT5_3893_S16


title: STR, Virus, Day 3, Rep 4

value: Day 3


title: 9L_M_1049


title: 9L_M_1048


title: AAVS1_Day10_2

description:
RNAseq library
D10_AAVS1_3881_S4


title: AAVS1_Day10_1

description:
RNAseq library
D10_AAVS1_3875_S12


title: MTX, Virus, Day 5, Rep 1

value: motor cortex

value: Day 5


title: SUPT5H_Day6_3

description:
RNAseq library
D6_SPT5_3893_S14

value: differntiation in culture Day 6


title: 9L_M_1047


title: DSRCT-4 Warm Dissociation

description: 10x Genomics


title: STR, Virus, Day 3, Rep 2

value: Infected with VEEV-TC


title: DSRCT-4 Nuclei Isolation

description: 10x Genomics


title: SUPT5H_colony3

description:
RNAseq library
PREP0081_DMart11435A_G01v1_FW_3_S5

value: progenitors


title: DSRCT-4 Cold Dissociation

description: 10x Genomics

value: DSRCT cell

value: Cold


title: STR, Virus, Day 3, Rep 1


title: DSRCT-1 Warm Dissociation

description: 10x Genomics

value: Warm


title: 9L_M_1045


title: 9L_M_1046


title: SUPT5H_colony10

description:
RNAseq library
PREP0081_DMart11435A_D02v1_RV_10_S7

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: DSRCT-1 Nuclei Isolation

description: 10x Genomics

value: PDX


title: DSRCT-2 Cold Dissociation Replicate 1

description: 10x Genomics


title: STR, Virus, Day 1, Rep 3

value: Day 1


title: AAVS1_colony23

description:
RNAseq library
PREP0081_DMart11435A_D01v1_AAVS1_23_S3

value: AAVS1 gRNA


title: 9L_M_1044


title: DSRCT-1 Cold Dissociation

description: 10x Genomics


title: STR, Virus, Day 1, Rep 2

value: Brain


title: STR, Virus, Day 3, Rep 3


title: 9L_M_1043


title: MTX, Virus, Day 6, Rep 4

value: Day 6


title: AAVS1_colony20

description:
RNAseq library
PREP0081_DMart11435A_C01v1_AAVS1_20_S2


title: 9L_M_1042


title: SUPT5H_colony2

description:
RNAseq library
PREP0081_DMart11435A_F01v1_FW_2_S4

value: SUPT5H gRNA


title: AAVS1_colony12

description:
RNAseq library
PREP0081_DMart11435A_A01v1_AAVS1_12_S1


title: 9L_M_1041


title: PIR, Virus, Day 7, Rep 3

value: piriform cortex

value: Day 7


title: D11b

description: NETseq library

data_processing:
Alignement with STAR (custom scripts available at https://github.com/churchmanlab)
Read counts of protein coding genes using featureCounts
Metagene analysis (custom scripts available at https://github.com/churchmanlab)
Pausing indices (custom scripts available at https://github.com/churchmanlab)
Assembly: GRCh38
Supplementary files format and content: OverlapMatrix*.txt files contain counts at bp positions around TSS
Supplementary files format and content: *.csv files contain read counts obtained from featureCounts on bam files
Library strategy: NET-seq

molecule: nuclear RNA

extract_protocol:
Qiagen miRNeasy
NETseq library preperation (https://dx.doi.org/10.17504/protocols.io.bpymmpu6)

value: differntiation in culture Day 11

value: WT


title: Astrocytes_#8_2_Primary_Rep3_P9_Bulk

type: genomic

city: San Diego

first: Morgan

middle: E.

last: Levine

address: 5510 Morehouse Dr

institute: Altos Labs

description:
Sample#8_2_Astrocytes_Primary_21yr_male_Replicate3_Passage9_Bulk
205103220176_R04C01

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation850 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
minfi package in R
Average beta, with noob normalization

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were seeded at 8,000 cells/cm2 with appropriate growth media and supplements (complete astrocyte medium, containing amino acids, vitamins, hormones, trace minerals, 2% fetal bovine serum and 1% PEN/STREP in HEPES pH 7.4 bicarbonate buffer, ScienCell #1801) to promote cell adhesion and growth. Of note, Poly-L-Lysine was not required for adequate cell adhesion. Cells were grown under normoxic conditions (20% O2, 5% CO2) at 37°C. Cells were split using 0.05% Trypsin-EDTA (Gibco, #25300-54).

extract_protocol: Genomic DNA was extracted using the DNAeasy Blood and Tissue Kit (Qiagen #69504) with proteinase K and RNAse A treatment. Samples were eluted with 200 µl of kit’s elution buffer. . Following final elution, DNA was verified using nanodrop (Thermo Scientific) and Qubit fluorometer (Invitrogen). Spin concentration was used as necessary with low DNA content samples. Prior to library preparation we used a Qubit fluorometer (Invitrogen) to quantify the extracted genomic DNA.

treatment_protocol: Primary and fetal hTERT-immortalized astrocytes were serially passaged and split a total of 8 and 15 times respectively. Cells were split when they reached approximately 90% confluence or when static growth was achieved. Live cells were counted using the Invitrogen Countess II and cell counting chamber slide with trypan blue. Cumulative population doubling (cPD) was calculated using the initial and final cell density, as determined by the countess (2x=FD/ID, where x=population doubling, FD=final cell density and ID=initial cell density).

value: primary astrocytes

tag: name

tag: sample number

tag: replicate

tag: days

tag: passage

tag: cpd

tag: fetal

tag: htert

tag: primary

tag: Sex

value: male

tag: source age (years)


title: STR, Virus, Day 1, Rep 1

tag: tissue

tag: brain region

value: striatum

tag: timepoint(dpi)

tag: genotype

tag: treatment

value: Infected with VEEV-TC


title: 9L_M_1040

tag: age

tag: strain


title: Astrocytes_#10_2_Primary_Rep2_P10_Bulk

description:
Sample#10_2_Astrocytes_Primary_21yr_male_Replicate2_Passage10_Bulk
205103220167_R06C01

tag: cell type

tag: name

tag: sample number


title: 9L_M_104


title: Astrocytes_#5_2_Primary_Rep3_P8_Bulk

description:
Sample#5_2_Astrocytes_Primary_21yr_male_Replicate3_Passage8_Bulk
205103220176_R02C01

tag: replicate

tag: days

tag: passage


title: PIR, Virus, Day 7, Rep 2


title: Astrocytes_#7_2_Primary_Rep2_P9_Bulk

description:
Sample#7_2_Astrocytes_Primary_21yr_male_Replicate2_Passage9_Bulk
205103220167_R02C01

tag: cpd

tag: fetal

tag: htert


title: STR, Virus, Day 1, Rep 4


title: Astrocytes_#6_2_Primary_Rep1_P9_Bulk

description:
Sample#6_2_Astrocytes_Primary_21yr_male_Replicate1_Passage9_Bulk
205103220176_R07C01

tag: primary

tag: Sex

tag: source age (years)


title: D10b

description: NETseq library

tag: tissue

tag: de-identified donor

tag: developmental stage

value: differntiation in culture Day 10


title: 9L_M_1039

tag: brain region

tag: age


title: PIR, Virus, Day 7, Rep 1

tag: timepoint(dpi)

tag: genotype

tag: treatment


title: Astrocytes_#4_2_Primary_Rep2_P8_Bulk

description:
Sample#4_2_Astrocytes_Primary_21yr_male_Replicate2_Passage8_Bulk
205103220167_R01C01

tag: cell type

tag: name

tag: sample number

tag: replicate


title: Kacme_K562_2

city: Orange

first: Matthew

last: Simon

state: CT

address: 100 West Campus Drive, Ste MIC 231

department: Molecular Biophysics and Biochemistry

institute: Yale University

data_processing:
Reads were trimmed of adaptor sequences using Cutadapt.
Reads were aligned to dm6 or hg38 genome using Bowtie2 v2.2.9.
Peaks were called using MACS2 with default parameters.
Fold enrichment bigwig tracks were created using MACS2 bdgcamp compared to input control.
Assembly: dm6, hg38
Supplementary files format and content: bigwig files of fold enrichment tracks over input control
Supplementary files format and content: narrowPeak peak files from MACS2

source_name: Human leukemia derived cell line

extract_protocol:
20-30 million cells per IP were crosslinked with formaldehyde for 10 minutes. Nuclei were sonicated, lysates were clarified, and histone-DNA complexes were isolated with antibody.
Libraries were prepared using standard Illumina protocols.

tag: cell line

value: K562 cells

tag: antibody

value: In house Kacme

tag: experiment

value: ChIP-seq


title: PIR, Virus, Day 6, Rep 4


title: D08b

description: NETseq library

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: differntiation in culture Day 8


title: D09b

description: NETseq library

value: differntiation in culture Day 9


title: 9L_M_1038

tag: strain


title: PIR, Virus, Day 6, Rep 3

value: Brain

value: Day 6


title: D07b

description: NETseq library

value: differntiation in culture Day 7


title: 9L_M_1037


title: PIR, Virus, Day 7, Rep 4

value: piriform cortex

value: Day 7


title: D06b

description: NETseq library

value: differntiation in culture Day 6

value: WT


title: Astrocytes_#2_2_Primary_Rep3_P7_Bulk

description:
Sample#2_2_Astrocytes_Primary_21yr_male_Replicate3_Passage7_Bulk
205134960028_R03C01

value: primary astrocytes

tag: days

tag: passage

tag: cpd

tag: fetal

tag: htert

tag: primary

tag: Sex

value: male

tag: source age (years)


title: PIR, Virus, Day 6, Rep 2

tag: tissue

tag: brain region

tag: timepoint(dpi)

tag: genotype

tag: treatment

value: Infected with VEEV-TC


title: Astrocytes_#3_2_Primary_Rep1_P8_Bulk

description:
Sample#3_2_Astrocytes_Primary_21yr_male_Replicate1_Passage8_Bulk
205134960028_R01C01

tag: cell type

tag: name

tag: sample number

tag: replicate


title: 9L_M_1036

tag: age

tag: strain


title: PIR, Virus, Day 6, Rep 1


title: Astrocytes_#11_2_Primary_Rep3_P10_Bulk

description:
Sample#11_2_Astrocytes_Primary_21yr_male_Replicate3_Passage10_Bulk
205134960050_R04C01

tag: days

tag: passage

tag: cpd


title: D05b

description: NETseq library

tag: de-identified donor

tag: developmental stage

value: differntiation in culture Day 5


title: D04b

description: NETseq library

value: differntiation in culture Day 4


title: 9L_M_1035


title: D03b

description: NETseq library

value: differntiation in culture Day 3


title: PIR, Virus, Day 5, Rep 3

value: Day 5


title: 9L_M_1033


title: PIR, Virus, Day 5, Rep 2


title: D02b

description: NETseq library

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: differntiation in culture Day 2


title: D00b

description: NETseq library

value: differntiation in culture Day 0


title: Astrocytes_#40_Fetal_hTERT_Rep2_P14_Bulk

description:
Sample#40_Astrocytes_Fetal_hTERT_Replicate2_Passage14_Bulk
205103220156_R07C01

value: hTERT-immortalized astrocytes

tag: fetal

tag: htert

tag: primary

tag: Sex

tag: source age (years)


title: Astrocytes_#9_2_Primary_Rep1_P10_Bulk

description:
Sample#9_2_Astrocytes_Primary_21yr_male_Replicate1_Passage10_Bulk
205134960050_R02C01


title: 9L_M_1032

tag: brain region


title: Astrocytes_#60_Fetal_hTERT_Rep1_P21_Bulk

description:
Sample#60_Astrocytes_Fetal_hTERT_Replicate1_Passage21_Bulk
205103220156_R08C01

tag: cell type


title: PIR, Virus, Day 3, Rep 4

tag: tissue

value: Brain

tag: timepoint(dpi)

value: Day 3

tag: genotype

tag: treatment


title: D10a

description: NETseq library

value: differntiation in culture Day 10


title: Astrocytes_#87_Primary_Rep3_P4_Bulk

description:
Sample#87_Astrocytes_Primary_21yr_male_Replicate3_Passage4_Bulk
205103220156_R06C01

tag: name

tag: sample number

tag: replicate


title: 9L_M_1030

tag: age

tag: strain


title: D11a

description: NETseq library

tag: de-identified donor

tag: developmental stage

value: differntiation in culture Day 11


title: Astrocytes_#38_Fetal_hTERT_Rep3_P13_Bulk

description:
Sample#38_Astrocytes_Fetal_hTERT_Replicate3_Passage13_Bulk
205103220156_R03C01

tag: days

tag: passage

tag: cpd

tag: fetal

tag: htert


title: PIR, Virus, Day 5, Rep 1

tag: brain region

value: piriform cortex


title: 9L_M_1031


title: 9L_M_1034


title: Astrocytes_#1_2_Primary_Rep2_P7_Bulk

description:
Sample#1_2_Astrocytes_Primary_21yr_male_Replicate2_Passage7_Bulk
205134960028_R08C01

tag: cell type

value: primary astrocytes

tag: primary

tag: Sex

tag: source age (years)


title: D08a

description: NETseq library

tag: tissue

value: differntiation in culture Day 8

tag: treatment

value: WT


title: Astrocytes_#45_Fetal_hTERT_Rep1_P16_Bulk

description:
Sample#45_Astrocytes_Fetal_hTERT_Replicate1_Passage16_Bulk
205107400007_R06C01

tag: name

tag: sample number

tag: replicate


title: PIR, Virus, Day 3, Rep 1

tag: timepoint(dpi)

tag: genotype

value: Infected with VEEV-TC


title: D09a

description: NETseq library

tag: de-identified donor

tag: developmental stage

value: differntiation in culture Day 9


title: 9L_M_103

tag: age

tag: strain


title: PIR, Virus, Day 3, Rep 3


title: 9L_M_1028


title: 9L_M_1029


title: PIR, Virus, Day 1, Rep 4

value: Day 1


title: D07a

description: NETseq library

value: differntiation in culture Day 7


title: Astrocytes_#53_Fetal_hTERT_Rep3_P18_Bulk

description:
Sample#53_Astrocytes_Fetal_hTERT_Replicate3_Passage18_Bulk
205107400007_R05C01

tag: days

tag: passage

tag: cpd

tag: fetal

tag: htert


title: PIR, Virus, Day 5, Rep 4

tag: brain region

value: Day 5


title: PIR, Virus, Day 1, Rep 3

tag: tissue


title: 9L_M_1027


title: Astrocytes_#81_Primary_Rep1_P2_Bulk

description:
Sample#81_Astrocytes_Primary_21yr_male_Replicate1_Passage2_Bulk
205107400007_R02C01

tag: cell type

tag: primary

tag: Sex

value: male

tag: source age (years)


title: 9L_M_1026


title: D06a

description: NETseq library

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: differntiation in culture Day 6

tag: treatment


title: D05a

description: NETseq library

value: differntiation in culture Day 5


title: Astrocytes_#70_Fetal_hTERT_Rep2_P24_Bulk

description:
Sample#70_Astrocytes_Fetal_hTERT_Replicate2_Passage24_Bulk
205103220156_R04C01

value: hTERT-immortalized astrocytes

tag: name

tag: sample number

tag: replicate


title: Astrocytes_#77_Fetal_hTERT_Rep3_P26_Bulk

description:
Sample#77_Astrocytes_Fetal_hTERT_Replicate3_Passage26_Bulk
205107400007_R01C01


title: PIR, Virus, Day 1, Rep 2

value: Brain

tag: timepoint(dpi)

tag: genotype


title: D04a

description: NETseq library

tag: de-identified donor

tag: developmental stage

value: differntiation in culture Day 4


title: Astrocytes_#49_Fetal_hTERT_Rep2_P17_Bulk

description:
Sample#49_Astrocytes_Fetal_hTERT_Replicate2_Passage17_Bulk
205134960060_R08C01

tag: days

tag: passage

tag: cpd


title: 9L_M_1025

tag: brain region

tag: age

tag: strain


title: PIR, Virus, Day 3, Rep 2

tag: tissue

value: piriform cortex

value: Day 3


title: Astrocytes_#85_Primary_Rep1_P4_Bulk

description:
Sample#85_Astrocytes_Primary_21yr_male_Replicate1_Passage4_Bulk
205134960060_R07C01

tag: cell type

value: primary astrocytes

tag: fetal

tag: htert

tag: primary

tag: Sex


title: D03a

description: NETseq library

value: differntiation in culture Day 3

tag: treatment

value: WT


title: 9L_M_1024


title: PIR, Virus, Day 1, Rep 1

tag: timepoint(dpi)

value: Infected with VEEV-TC


title: Astrocytes_#67_Fetal_hTERT_Rep2_P23_Bulk

description:
Sample#67_Astrocytes_Fetal_hTERT_Replicate2_Passage23_Bulk
205134960060_R04C01

tag: name

tag: sample number

tag: replicate

tag: source age (years)


title: MOB, Virus, Day 7, Rep 4

value: main olfactory bulb

value: Day 7

tag: genotype


title: 9L_M_1023


title: MOB, Virus, Day 7, Rep 3


title: Astrocytes_#91_Primary_Rep1_P6_Bulk

description:
Sample#91_Astrocytes_Primary_21yr_male_Replicate1_Passage6_Bulk
205134960060_R03C01

tag: days

tag: passage

tag: cpd


title: D01a

description: NETseq library

tag: de-identified donor

tag: developmental stage

value: differntiation in culture Day 1


title: 9L_M_1022

tag: brain region

tag: age

tag: strain


title: D02a

description: NETseq library

tag: tissue

tag: cell type

value: differntiation in culture Day 2


title: 9L_M_1021


title: MOB, Virus, Day 7, Rep 2

tag: treatment


title: D00a

description: NETseq library

value: Bone Marrow

value: differntiation in culture Day 0


title: 9L_M_1020


title: Astrocytes_#58_Fetal_hTERT_Rep2_P20_Bulk

description:
Sample#58_Astrocytes_Fetal_hTERT_Replicate2_Passage20_Bulk
205134960060_R01C01

tag: fetal

tag: htert

tag: primary

tag: Sex


title: MOB, Virus, Day 7, Rep 1

tag: timepoint(dpi)


title: Astrocytes_#89_Primary_Rep2_P5_Bulk

description:
Sample#89_Astrocytes_Primary_21yr_male_Replicate2_Passage5_Bulk
205107400016_R08C01

tag: name

tag: sample number

tag: replicate

value: male

tag: source age (years)


title: Trip_30_2

description: NETseq library

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

tag: de-identified donor

value: differntiation in culture Day 8

value: Triptolide


title: MOB, Virus, Day 6, Rep 4

value: Brain

value: Day 6

tag: genotype


title: MOB, Virus, Day 6, Rep 3

tag: brain region


title: 9L_M_102

tag: age


title: Astrocytes_#46_Fetal_hTERT_Rep2_P16_Bulk

description:
Sample#46_Astrocytes_Fetal_hTERT_Replicate2_Passage16_Bulk
205107400016_R05C01

value: hTERT-immortalized astrocytes

tag: days

tag: passage

tag: cpd


title: 9L_M_1019

tag: strain


title: Astrocytes_#59_Fetal_hTERT_Rep3_P20_Bulk

description:
Sample#59_Astrocytes_Fetal_hTERT_Replicate3_Passage20_Bulk
205107400016_R04C01

tag: cell type

tag: fetal


title: MOB, Virus, Day 6, Rep 2

tag: tissue

tag: treatment


title: SPI21_120_2

description: NETseq library

tag: developmental stage


title: 9L_M_1018


title: SPI21_120_1

description: NETseq library


title: MOB, Virus, Day 6, Rep 1

tag: timepoint(dpi)


title: 9L_M_1017


title: Astrocytes_#94_Primary_Rep1_P7_Bulk

description:
Sample#94_Astrocytes_Primary_21yr_male_Replicate1_Passage7_Bulk
205107400016_R03C01

value: primary astrocytes

tag: name

tag: sample number

tag: htert

tag: primary

tag: Sex


title: Astrocytes_#71_Fetal_hTERT_Rep3_P24_Bulk

description:
Sample#71_Astrocytes_Fetal_hTERT_Replicate3_Passage24_Bulk
205134960171_R07C01

tag: replicate

tag: source age (years)


title: MOB, Virus, Day 5, Rep 4

tag: brain region

value: Day 5

tag: genotype


title: SPI18_120_1

description: NETseq library

tag: de-identified donor


title: MOB, Virus, Day 5, Rep 3


title: Astrocytes_#44_Fetal_hTERT_Rep3_P15_Bulk

description:
Sample#44_Astrocytes_Fetal_hTERT_Replicate3_Passage15_Bulk
205134960171_R05C01

tag: days

tag: passage

tag: cpd


title: 9L_M_1014

tag: age

tag: strain


title: DRB_30_2

description: NETseq library

tag: tissue

tag: cell type

tag: developmental stage

tag: treatment

value: DRB


title: Astrocytes_#90_Primary_Rep3_P5_Bulk

description:
Sample#90_Astrocytes_Primary_21yr_male_Replicate3_Passage5_Bulk
205134960171_R04C01

tag: name

tag: sample number

tag: fetal

tag: htert


title: Trip_30_1

description: NETseq library


title: MOB, Virus, Day 5, Rep 2

tag: timepoint(dpi)

value: Infected with VEEV-TC


title: Astrocytes_#66_Fetal_hTERT_Rep1_P23_Bulk

description:
Sample#66_Astrocytes_Fetal_hTERT_Replicate1_Passage23_Bulk
205134960171_R03C01

tag: replicate

tag: primary

tag: Sex

tag: source age (years)


title: MOB, Virus, Day 5, Rep 1

tag: brain region

value: main olfactory bulb

tag: genotype


title: DRB_30_1

description: NETseq library

tag: de-identified donor


title: Astrocytes_#86_Primary_Rep2_P4_Bulk

description:
Sample#86_Astrocytes_Primary_21yr_male_Replicate2_Passage4_Bulk
205134960171_R02C01

tag: days

tag: passage

tag: cpd


title: 9L_M_1012

tag: age

tag: strain


title: 9L_M_1013


title: DMSO_30_2

description: NETseq library

tag: tissue

tag: cell type

tag: developmental stage

tag: treatment

value: DMSO


title: 9L_M_1011


title: 9L_M_1010


title: Astrocytes_#92_Primary_Rep2_P6_Bulk

description:
Sample#92_Astrocytes_Primary_21yr_male_Replicate2_Passage6_Bulk
205107400018_R05C01

tag: name

tag: sample number

tag: fetal

tag: htert


title: Astrocytes_#82_Primary_Rep1_P3_Bulk

description:
Sample#82_Astrocytes_Primary_21yr_male_Replicate1_Passage3_Bulk
205134960171_R01C01

tag: replicate

tag: primary

tag: Sex

tag: source age (years)


title: DMSO_120_2

description: NETseq library

tag: de-identified donor


title: 9L_M_101

tag: brain region


title: MOB, Virus, Day 3, Rep 3

tag: timepoint(dpi)

value: Day 3

tag: genotype


title: MOB, Virus, Day 3, Rep 4


title: Astrocytes_#69_Fetal_hTERT_Rep1_P24_Bulk

description:
Sample#69_Astrocytes_Fetal_hTERT_Replicate1_Passage24_Bulk
205107400018_R04C01

tag: days

tag: passage

tag: cpd


title: DMSO_30_1

description: NETseq library

tag: tissue

tag: cell type

tag: developmental stage


title: MOB, Virus, Day 3, Rep 1

tag: treatment


title: Astrocytes_#48_Fetal_hTERT_Rep1_P17_Bulk

description:
Sample#48_Astrocytes_Fetal_hTERT_Replicate1_Passage17_Bulk
205107400018_R03C01

tag: name

tag: sample number

tag: fetal


title: 9L_M_1009

tag: age

tag: strain


title: 9L_M_1015


title: 3850_SPT5

description: NETseq library

value: SUPT5H gRNA


title: MOB, Virus, Day 1, Rep 4

value: Day 1


title: Astrocytes_#83_Primary_Rep2_P3_Bulk

description:
Sample#83_Astrocytes_Primary_21yr_male_Replicate2_Passage3_Bulk
205107400018_R02C01

tag: replicate

tag: htert

tag: primary

tag: Sex

tag: source age (years)


title: MOB, Virus, Day 1, Rep 3

tag: brain region

tag: timepoint(dpi)

tag: genotype


title: Astrocytes_#84_Primary_Rep3_P3_Bulk

description:
Sample#84_Astrocytes_Primary_21yr_male_Replicate3_Passage3_Bulk
205107400018_R01C01

tag: days

tag: passage

tag: cpd


title: 9L_M_1008


title: 9L_M_1007


title: 3824_SPT5

description: NETseq library

tag: tissue

value: Bone Marrow

tag: cell type

tag: de-identified donor

tag: developmental stage

tag: treatment


title: MOB, Virus, Day 1, Rep 2


title: 3824_AAVS1

description: NETseq library

value: AAVS1 gRNA


title: MOB, Virus, Day 3, Rep 2


title: MOB, Virus, Day 1, Rep 1


title: 3817_SPT5

description: NETseq library

value: Hematopoietic Stem and Progenitor Cells (HSPCs)


title: Astrocytes_#43_Fetal_hTERT_Rep2_P15_Bulk

description:
Sample#43_Astrocytes_Fetal_hTERT_Replicate2_Passage15_Bulk
205134960059_R07C01

tag: name

tag: sample number

tag: fetal


title: Astrocytes_#56_Fetal_hTERT_Rep3_P19_Bulk

description:
Sample#56_Astrocytes_Fetal_hTERT_Replicate3_Passage19_Bulk
205134960059_R04C01

tag: replicate

tag: htert

tag: primary


title: 9L_M_1005

tag: brain region

tag: age

tag: strain


title: Astrocytes_#37_Fetal_hTERT_Rep2_P13_Bulk

description:
Sample#37_Astrocytes_Fetal_hTERT_Replicate2_Passage13_Bulk
205134960059_R06C01

tag: days

tag: Sex

tag: source age (years)


title: 9L_M_1003


title: CD8+ T cells 12d activation (H2O) donor 3

city: Amsterdam

first: Monika

middle: C

last: Wolkers

address: Plesmanlaan 125

department: Hematopoiesis

country: Netherlands

institute: Sanquin Blood foundation

data_processing:
Reads were quasi-mapped and quantified using Salmon (version 1.8), onto the transcriptome (ENSEMBL version 104).
Assembly: Human transcriptome (ENSEMBL version 104)
Supplementary files format and content: Count matrix in TPM (Output by Salmon)

source_name: Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from healthy donors from Cambridge Bioscience, National Health Service (NHS) Blood and Transplant (NHSBT: Addenbrooke’s Hospital, Cambridge, UK) or Sanquin (Amsterdam, NL). The study was performed according to the Declaration of Helsinki (seventh revision, 2013). Ethical approval was obtained from the East of England-Cambridge Central Research Ethics Committee (06/Q0108/281) and consent was obtained from all subjects. Written informed consent was obtained (Cambridge Bioscience, Cambridge, UK; NHSBT Cambridge, UK; Sanquin Research, Amsterdam, NL). Human CD8+ T cells were isolated either directly after blood donation (8-12 hrs after blood collection) or they were cryopreserved and used after cryopreservation. PBMCs were isolated through Ficoll-Paque PLUS density gradient separation (GE Healthcare). Cells were incubated in 21% oxygen, 5% carbon dioxide at 37 °C. Naïve CD8+ T cells were isolated by MACS Miltenyi (130-093-244) following manufacturer’s instructions.

extract_protocol:
The cells were lysed on RLT Buffer containing (1:100) β-Mercaptoethanol.
RNA-Seq libraries was prepared and sequenced by Active Motif (USA) on Illumina NextSeq 500 for 42 cycles (42nt paired-end reads).

treatment_protocol: CD8+ T cells were activated with aCD3/CD28 beads (1:1 beads-to-cell ratio) (11132D, Gibco) for 4 days. OE-S-2HG treatment and OE-R-2HG (H942595; H942596 Toronto Research Chemicals) started at day 0 and was at 0.4 mM concentration. Every second day, fresh complete RPMI media (52400-025; Gibco) containing 10% FBS, 1% penicillin-streptomycin and IL-2 (30 U/ml) and the appropriate amount of OE-S-2HG, OE-R-2HG or vehicle was added. The cells were collected for RNA-Seq analysis either on day 5 (3 donors) or on day 12 (3 different donors).

tag: individual

value: different donor 3

tag: tissue

value: Blood

value: CD8+ T cells

tag: time

value: 12d activation


title: Astrocytes_#64_Fetal_hTERT_Rep2_P22_Bulk

description:
Sample#64_Astrocytes_Fetal_hTERT_Replicate2_Passage22_Bulk
205134960059_R03C01

tag: cell type

value: hTERT-immortalized astrocytes

tag: passage

tag: cpd


title: 3817_AAVS1

description: NETseq library

tag: de-identified donor

tag: developmental stage

value: differntiation in culture Day 8

tag: treatment


title: 9L_M_1002


title: 3850_AAVS1

description: NETseq library


title: iPSC-astrocytes-and-neurons_ChR2-YFP_SCF042-03-01_5

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

institute: UK Dementia Research Institute at Cardiff University

description: transcript quantification in abundance.tsv file

data_processing:
Read quality control using FastQC and summarization with MultiQC.
Transcript abundaces were quantified using Kallisto for linux version 0.43.1 using the human transcriptome as a reference (cdna and ncrna from GRCh38, available through ensemble ftp, release 91).
Summarization at gene level with Tximport R library
Filtering out lowly expressed genes (with less than 5 TPM)
Differential expression analysis was perform using DeSeq2
Assembly: GRCh38 / Ensembl release 91
Supplementary files format and content: abundance.tsv contain transcript quantification, Ensembl transcript ID (target_id), length, effective length (eff_length), estimated counts (est_counts) and transcripts per million (tpm)
Supplementary files format and content: TPM_protein_coding_genes.tsv transcripts per million at gene level

source_name: Human iPSC-astrocyte and iPSC-neuron in co-culture

growth_protocol: Human iPSC-astrocytes and iPSC-neurons were differentiated separately, and then expressing a different fluorescent reporter in each cell population before they were combined to produce co-cultures

extract_protocol:
RNA was extracted (each 8-9ul at 150-400 ng/ul)
RNA samples were prepared for sequencing using standard poly-A isolation protocol (HiSeq 3000/4000 SBS Kit)

treatment_protocol: The long-term optogenetic stimulation consisted of 250 ms duration pulses, at intervals of 50 s, and continued for the entire 3-5 day period

tag: cell line

value: iPSC-derived astrocytes and iPSC-derived neurons

tag: genotype


title: iPSC-astrocytes-and-neurons_ChR2-YFP_SCF042-03-01_1

value: Human iPSC-astrocyte and iPSC-neuron in co-culture


title: iPSC-astrocytes-and-neurons_YFP-control_SCF042-03-01_3

value: YFP-control


title: iPSC-astrocytes-and-neurons_ChR2-YFP_SCF042-03-01_4


title: Astrocytes_#65_Fetal_hTERT_Rep3_P22_Bulk

description:
Sample#65_Astrocytes_Fetal_hTERT_Replicate3_Passage22_Bulk
205134960059_R02C01

tag: name

tag: sample number

tag: replicate

tag: fetal

tag: htert

tag: primary


title: Astrocytes_#51_Fetal_hTERT_Rep1_P18_Bulk

description:
Sample#51_Astrocytes_Fetal_hTERT_Replicate1_Passage18_Bulk
205103220121_R06C01

tag: days

tag: Sex

tag: source age (years)


title: iPSC-astrocytes-and-neurons_YFP-control_SCF042-03-01_2

tag: tissue

tag: cell type


title: 9L_M_1001

tag: brain region

tag: age

tag: strain


title: DMS0_120_1

description: NETseq library

tag: de-identified donor

tag: developmental stage

tag: treatment


title: Naive CD8+ T cells 12d donor 3

tag: individual

tag: time

value: control


title: 9L_M_1000


title: 9L_M_1006


title: SPI18_120_2

description: NETseq library


title: Astrocytes_#54_Fetal_hTERT_Rep1_P19_Bulk

description:
Sample#54_Astrocytes_Fetal_hTERT_Replicate1_Passage19_Bulk
205103220121_R05C01

tag: name

tag: sample number

tag: replicate

tag: passage

tag: cpd


title: iPSC-astrocytes-and-neurons_YFP-control_SCF042-03-01_1

tag: cell line

tag: genotype


title: 9L_M_1004


title: CD8+ T cells 12d activation (H2O) donor 2

value: different donor 2

tag: tissue


title: iPSC-astrocytes-and-neurons_ChR2-YFP_SBAD-03-01_1

tag: cell type

value: Ctrl


title: 9L_M_10

tag: brain region


title: CD8+ T cells 12d activation (S2HG) donor 2


title: 9L_M_100

tag: age


title: Astrocytes_#36_Fetal_hTERT_Rep1_P13_Bulk

description:
Sample#36_Astrocytes_Fetal_hTERT_Replicate1_Passage13_Bulk
205103220121_R03C01

tag: days

tag: fetal

tag: htert

tag: primary

tag: Sex

tag: source age (years)


title: CD8+ T cells 12d activation (S2HG) donor 3

tag: individual

tag: treatment

tag: time


title: Astrocytes_#62_Fetal_hTERT_Rep3_P21_Bulk

description:
Sample#62_Astrocytes_Fetal_hTERT_Replicate3_Passage21_Bulk
205103220121_R02C01

tag: name

tag: sample number

tag: replicate

tag: passage


title: CD8+ T cells 12d activation (R2HG) donor 3

tag: tissue


title: iPSC-astrocytes-and-neurons_YFP-control_SBAD-03-01_3

tag: cell line

tag: cell type

tag: genotype


title: 9L_M_1

tag: brain region

tag: age

tag: strain


title: 9L_M_0


title: Astrocytes_#88_Primary_Rep1_P5_Bulk

description:
Sample#88_Astrocytes_Primary_21yr_male_Replicate1_Passage5_Bulk
205134960027_R08C01

value: primary astrocytes

tag: days

tag: cpd

tag: fetal

tag: htert

tag: primary

value: male


title: Naive CD8+ T cells 12d donor 2

tag: individual

tag: treatment

tag: time


title: Astrocytes_#50_Fetal_hTERT_Rep3_P17_Bulk

description:
Sample#50_Astrocytes_Fetal_hTERT_Replicate3_Passage17_Bulk
205134960027_R06C01

tag: name

tag: sample number

tag: replicate

tag: Sex

tag: source age (years)


title: CD8+ T cells 12d activation (H2O) donor 1

value: different donor 1

tag: tissue

tag: cell type


title: CD8+ T cells 12d activation (S2HG) donor 1


title: Astrocytes_#35_Fetal_hTERT_Rep1_P12_Bulk

description:
Sample#35_Astrocytes_Fetal_hTERT_Replicate1_Passage12_Bulk
205134960027_R05C01

tag: passage


title: Astrocytes_#74_Fetal_hTERT_Rep3_P25_Bulk

description:
Sample#74_Astrocytes_Fetal_hTERT_Replicate3_Passage25_Bulk
205134960027_R04C01


title: Astrocytes_#52_Fetal_hTERT_Rep2_P18_Bulk

description:
Sample#52_Astrocytes_Fetal_hTERT_Replicate2_Passage18_Bulk
205103220121_R04C01


title: iPSC-astrocytes-and-neurons_ChR2-YFP_SBAD-02-01_6

tag: cell line

tag: genotype


title: iPSC-astrocytes-and-neurons_ChR2-YFP_SBAD-02-01_5


title: iPSC-astrocytes-and-neurons_YFP-control_SBAD-03-01_1


title: Astrocytes_#42_Fetal_hTERT_Rep1_P15_Bulk

description:
Sample#42_Astrocytes_Fetal_hTERT_Replicate1_Passage15_Bulk
205134960027_R03C01

tag: days

tag: cpd


title: iPSC-astrocytes-and-neurons_ChR2-YFP_SBAD-02-01_4


title: Naive CD8+ T cells 12d donor 1


title: CD8+ T cells 12d activation (R2HG) donor 2


title: Astrocytes_#79_Fetal_hTERT_Rep2_P27_Bulk

description:
Sample#79_Astrocytes_Fetal_hTERT_Replicate2_Passage27_Bulk
205134960027_R02C01

tag: fetal

tag: htert


title: iPSC-astrocytes-and-neurons_YFP-control_SBAD-03-01_4


title: Eif4a1 KO 1

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

data_processing:
RNA sequencing data were trimmed using TrimGalore (v0.6.6; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and quality checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Reads were mapped to the GRCm39 mouse genome build using HISAT2(v2.1.0; https://doi.org/10.1038/nmeth.3317), suppressing soft-clipping, unpaired or discordant alignments and taking into account known splice sites from the Ensembl GRCm39 v103 annotation release.
Raw read counts were generated using Seqmonk (v1.48.2.devel; https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) over mRNA features with merged isoforms, using the Ensembl GRCm39 v105 annotation, assuming opposing strand-specific, paired reads.
TPM were calculated using Stringtie(v2.1.1; https://doi.org/10.1038/nbt.3122), using the Ensembl GRCm39 v105 annotation
Assembly: GRCm39
Supplementary files format and content: Raw_counts_all.txt - tab-delimited text file containing gene names and IDs, with the raw read counts over mRNA features for each sample, generated using Seqmonk.
Supplementary files format and content: TPM_all.txt - tab-delimited text file containing gene names and IDs, together with gene-level TPM, calculated using Stringtie.

source_name: Spleen

extract_protocol:
Single cell suspensions were first incubated with 2.4G2 followed by a biotinylated H-2Kd (SF1-1.1) antibody at room temperature in MACS buffer. The biotinylated CD40LB cells were then removed by incubation with anti-biotin microbeads (Militenyi) and passed through a LS column. The purified B-cells were washed twice with ice-cold PBS and pellets were frozen on dry ice. RNA was isolated from the purified B cells using the RNeasy Mini Kit (Qiagen) and its quality was assessed on a 2100 Bioanalyser (Agilent).
Libraries were generated from 100ng of total RNA using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (#E7760) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (#E6440) following manufacturer's instructions. cDNA quality was checked using Qubit dsDNA HS Assay Kit (Q32854) and Agilent DNA 5000 tapestation reagents (5067-5588; 5067-5589). Samples were pooled at equimolar quantities, and sequenced on a Novaseq 6000 using one lane of an S1 flowcell, as paired end 50bp (PE50) reads.

treatment_protocol: Irradiated (120Gy) CD40LB (https://doi.org/10.1038/ncomms1475) were plated at a density of 5E04 per ml overnight. Splenic B cells from mice aged 8-12 weeks were isolated from single cell suspension using a B cell isolation kit (Cat. # 130-090-862 from Miltenyi). B cells were plated at 5E05 per ml in RPMI 1640 Dutch modified media (Thermo Scientific) supplemented with 10% FBS (Gibco), 1 x GlutaMAX (Gibco), 50 µM 2-mercaptoethanol (Thermo Scientific), 100 units/ml penicillin, and 100 μg/ml streptomycin (Thermo Scientific) and 40 ng/ml mIL-4 (PeproTech 214–14), and cultured for 24h.

tag: strain

value: Spleen

value: B cells

value: Eif4a1fl/fl CD23-cre

value: 24h activation with CD40LB

value: Male

tag: batch

value: A


title: Eif4a1 KO 3

tag: treatment

value: B


title: Eif4a1 KO 2

value: Female


title: Eif4a1 KO 4


title: iPSC-astrocytes-and-neurons_ChR2-YFP_SBAD-02-01_3

value: iPSC-derived astrocytes and iPSC-derived neurons


title: iPSC-astrocytes-and-neurons_YFP-control_SBAD-03-01_2

value: Human iPSC-astrocyte and iPSC-neuron in co-culture


title: CD8+ T cells 5d activation (R2HG) donor 3

tag: individual

value: donor 3

value: Blood

value: CD8+ T cells

tag: time

value: 5d activation


title: Astrocytes_#41_Fetal_hTERT_Rep3_P14_Bulk

description:
Sample#41_Astrocytes_Fetal_hTERT_Replicate3_Passage14_Bulk
205134960057_R05C01

value: hTERT-immortalized astrocytes

tag: name

tag: sample number

tag: replicate

tag: primary


title: CD8+ T cells 5d activation (H2O) donor 3

tag: tissue

tag: cell type


title: iPSC-astrocytes-and-neurons_ChR2-YFP_SBAD-02-01_2

tag: cell line

value: Ctrl


title: Astrocytes_#57_Fetal_hTERT_Rep1_P20_Bulk

description:
Sample#57_Astrocytes_Fetal_hTERT_Replicate1_Passage20_Bulk
205134960057_R08C01

tag: passage

tag: Sex

tag: source age (years)


title: Ctrl 2

tag: genotype

value: Eif4a1+/+ CD23-cre


title: Ctrl 3

value: Spleen


title: iPSC-astrocytes-and-neurons_ChR2-YFP_SBAD-02-01_1


title: CD8+ T cells 12d activation (R2HG) donor 1

value: different donor 1

value: 12d activation


title: Ctrl 1

value: B cells

value: 24h activation with CD40LB


title: CD8+ T cells 5d activation (S2HG) donor 2

value: donor 2


title: Astrocytes_#76_Fetal_hTERT_Rep2_P26_Bulk

description:
Sample#76_Astrocytes_Fetal_hTERT_Replicate2_Passage26_Bulk
205134960057_R01C01

tag: days

tag: cpd

tag: fetal

tag: htert


title: iPSC-astrocytes-and-neurons_YFP-control_SBAD-02-01_6

tag: treatment

value: YFP-control


title: Astrocytes_#68_Fetal_hTERT_Rep3_P23_Bulk

description:
Sample#68_Astrocytes_Fetal_hTERT_Replicate3_Passage23_Bulk
205103220113_R08C01


title: CD8+ T cells 5d activation (R2HG) donor 2

tag: individual

tag: time


title: KO3

first: Li-Fan

last: Lu

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

data_processing:
Reads from all libraries were mapped to the mouse genome (mm10) using STAR (v2.2.0c). To calculate gene expression, read counts in the exons of RefSeq transcripts where calculated using HOMER
Assembly: mm10
Supplementary files format and content: RPKM values for each Sample

source_name: miR-15/16-deficient Treg cells

extract_protocol:
total RNA (including small RNAs) was extracted with the miRNeasy kit (Qiagen) from FACS-sorted CD4+Foxp3+ Treg cells isolated from indicated mice
Multiplexed libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit. Libraries were sequenced on the Illumina NovaSeq 6000 according to the manufacturer's instructions.

tag: strain

value: CD4+Foxp3+ Treg cells

value: miR-15/16 deficient


title: CD8+ T cells 5d activation (H2O) donor 2


title: KO2


title: Astrocytes_#47_Fetal_hTERT_Rep3_P16_Bulk

description:
Sample#47_Astrocytes_Fetal_hTERT_Replicate3_Passage16_Bulk
205103220113_R06C01

tag: name

tag: sample number

tag: replicate


title: CD8+ T cells 5d activation (S2HG) donor 1

value: donor 1

tag: tissue

tag: cell type


title: iPSC-astrocytes-and-neurons_YFP-control_SBAD-02-01_4

description: transcript quantification in abundance.tsv file

value: Human iPSC-astrocyte and iPSC-neuron in co-culture

tag: cell line

value: iPSC-derived astrocytes and iPSC-derived neurons


title: CD8+ T cells 5d activation (S2HG) donor 3

value: donor 3

value: Blood

value: CD8+ T cells


title: KO1


title: CD8+ T cells 5d activation (R2HG) donor 1

value: 5d activation


title: iPSC-astrocytes-and-neurons_YFP-control_SBAD-02-01_3

value: Ctrl


title: Astrocytes_#73_Fetal_hTERT_Rep2_P25_Bulk

description:
Sample#73_Astrocytes_Fetal_hTERT_Replicate2_Passage25_Bulk
205103220113_R01C01

value: hTERT-immortalized astrocytes

tag: passage

tag: primary

tag: Sex


title: Ctrl 4

value: Spleen

tag: genotype

value: Eif4a1+/+ CD23-cre

value: Female

tag: batch

value: B


title: Astrocytes_#61_Fetal_hTERT_Rep2_P21_Bulk

description:
Sample#61_Astrocytes_Fetal_hTERT_Replicate2_Passage21_Bulk
205103220172_R07C01

tag: days

tag: cpd

tag: fetal

tag: source age (years)


title: WT3

source_name: WT Treg cells

value: WT


title: siGPR153_3_EXPB

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

data_processing:
Basecalling RTA 2.4.11, Illumina instrument run time analysis software
Demultiplexing, Bcl2fastq v2.17
Filtering (Adaptor and quality), Cutadapt 1.18
Alignment, STAR 2.7.0f
Counts were calculated in PartekFlow v8 and processed with R version 4.0.3  using the edgeR 3.31.4 R package. Batch effects from different sequencing experiments were removed using the removeBatchEffect R function from the limma 3.45.14 R package using siCon samples as reference. Differential expression analysis against siCon cells was performed using the limma 3.45.14 R package.
Assembly: hg19
Supplementary files format and content: "Gene_counts-no batch corrected.txt" contains the raw gene counts without normalization or batch correction for different experiments
Supplementary files format and content: "logcpm_TMM_normalized_GPCR_BatchCorrected.txt" contains normalized and batch corrected counts

source_name: skin

growth_protocol: Cells were cultured at 37°C in the presence of 5% CO2 and cultured in EPILIFE medium (Life Technologies) with Human Keratinocyte Growth Supplement (HKGS, Life Technologies).

extract_protocol:
RNA was isolated and processed using RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cells were lysed using the Precellys lysing kit (Bertin Instruments).
TruSeq mRNA Prep Kit RS-122-2101

treatment_protocol: Cells were transfected with the corresponding siRNAs one day after plating and were harvested 72hs after transfection. siRNAs were from Dharmacon/ Horizon Discovery; ON-TARGET plus SMARTpool: LTB4R (L-005653-00), HCAR3 (L-005628-02), GPR153 (L-027388-00), GPR137 (L-005439-01), and non-targeting control siRNA (D-001810-10). siRNA was transfected at a concentration of 15 pmol/well for 6-well plates using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s instructions.

value: Primary neonatal pooled human keratinocytes

value: skin

tag: treatment

value: EXPB


title: siGPR153_2_EXPB


title: WT1

tag: strain

value: CD4+Foxp3+ Treg cells


title: Astrocytes_#93_Primary_Rep3_P6_Bulk

description:
Sample#93_Astrocytes_Primary_21yr_male_Replicate3_Passage6_Bulk
205103220172_R06C01

value: primary astrocytes

tag: name

tag: htert

value: male


title: glioblastoma stem cells, U3086

first: Helene

last: Damhofer

address: 237 Fulham Road

department: Cancer Biology

institute: The Institute of Cancer Research

data_processing:
Reads were trimmed and mapped to the human hg19 genome using HISAT2 (v2.2.1) with default parameters. Transcript count matrix was generated by using featureCounts (subread package 2.0.1) with gencode.v19.annotation.gtf for transcript annotation.
Assembly: hg19/GRCh37.p13
Supplementary files format and content: tab-delimited text files including Ensemble gene ID (EnsembleID) and raw feature counts for each cell line sample

source_name: glioblastoma multiforme

growth_protocol: Glioma stem cells were cultured adherently in serum-free neural stem cell medium (DMEM/F12 + Neurobasal 1:1 mixture) supplemented with L-glutamine, 15mM HEPES, 55 mg/L sodium pyruvate, non-essential amino acids, 0.05 mg/ml BSA, 2ug/ml Heparin, penicillin/streptomycin, N2, B27,  10 ng/ml human EGF and 10 ng/ml human FGF-2 on PDL and Laminin I (Cultrex, R&D) precoated dishes. Detachment from plates and passaging of glioma stem cells was performed with Accutase (Sigma). Cells were grown under standard aseptic tissue culture conditions at 37deg Celsius and 5% CO2.

extract_protocol:
Total RNA from glioma stem cells was extracted using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was determined on a Nanodrop (Thermo Fisher) and RNA quality was confirmed on a Bioanalyzer 2100 RNA 600 Nano Chip (Agilent) to have a RIN value of >9.
Libraries for next-generation sequencing were prepared with 500ng total RNA input using Illumina TruSeq RNA Library preparation kit v2 according to manufacturer’s protocol

treatment_protocol: Glioma stem cells were seeded at 30-40% confluency, cultured for 48h under regular growth condition and were lysed  in the tissue culture plate for RNA extraction in RLTplus buffer (Qiagen) freshly supplemented with  beta-mercaptoethanol.

value: glioblastoma multiforme

value: glioblastoma stem cells


title: WT2


title: iPSC-astrocytes-and-neurons_YFP-control_SBAD-02-01_2

value: Human iPSC-astrocyte and iPSC-neuron in co-culture

value: iPSC-derived astrocytes and iPSC-derived neurons

value: YFP-control


title: Astrocytes_#55_Fetal_hTERT_Rep2_P19_Bulk

description:
Sample#55_Astrocytes_Fetal_hTERT_Replicate2_Passage19_Bulk
205103220172_R05C01

value: hTERT-immortalized astrocytes

tag: sample number

tag: replicate


title: siGPR153_1_EXPB

tag: cell type

tag: tissue


title: iPSC-astrocytes-and-neurons_YFP-control_SBAD-02-01_5

tag: cell line

value: Ctrl


title: Organoid cells, HER2 and PIK3CA Mutation, HP5

city: St. Louis

first: Yirui

last: Sun

state: MO

address: 660 S Euclid Ave

institute: Washington University in St. Louis

data_processing:
Illumina’s bcl2fastq software (v2.20)
RNA-seq reads were then aligned to the Ensembl release 96 top-level assemblies with STAR (v2.0.4b).Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCounts (v1.4.5).
Sequencing performance was assessed for the total number of aligned reads, the total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC (v2.3).
All the gene counts were imported into the R/Bioconductor package DESeq2 (v1.33.5). Mutation groups were modeled as the variates for differential gene expression testing. The raw counts have normalized with the median of ratios method provided by DESeq2 and the effect size shrinkage was performed using the ashr method.
Assembly: mm10
Supplementary files format and content: tab-delimited text files

source_name: tumor breast

growth_protocol: Organoid cells are cultured in the medium supply with advanced Dulbecco’s modified Eagle medium/F12, penicillin/streptomycin, 10 mmol/L HEPES, Glutamax, 1 × B27 [all from Thermo Fisher Scientific], 125 µM N-acetyl-cysteine (Sigma), 50 ng/ml murine epidermal growth factor (EGF, Invitrogen), 10% Rspo1- Noggin- conditioned medium.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: tumor breast

value: Organoid cells

value: HER2 and PIK3CA Mutation


title: Astrocytes_#72_Fetal_hTERT_Rep1_P25_Bulk

description:
Sample#72_Astrocytes_Fetal_hTERT_Replicate1_Passage25_Bulk
205103220172_R04C01

tag: passage

tag: primary


title: Astrocytes_#39_Fetal_hTERT_Rep1_P14_Bulk

description:
Sample#39_Astrocytes_Fetal_hTERT_Replicate1_Passage14_Bulk
205103220113_R04C01

tag: Sex


title: glioblastoma stem cells, U3047


title: WT4

tag: genotype

value: WT


title: glioblastoma stem cells, U3031


title: Astrocytes_#63_Fetal_hTERT_Rep1_P22_Bulk

description:
Sample#63_Astrocytes_Fetal_hTERT_Replicate1_Passage22_Bulk
205103220172_R03C01

tag: days


title: siHCAR3_2_EXPB

value: Primary neonatal pooled human keratinocytes

tag: batch


title: Organoid cells, HER2 and PIK3CA Mutation, HP3


title: Astrocytes_#75_Fetal_hTERT_Rep1_P26_Bulk

description:
Sample#75_Astrocytes_Fetal_hTERT_Replicate1_Passage26_Bulk
205103220172_R02C01

tag: cpd

tag: fetal


title: siHCAR3_1_EXPB

value: skin

tag: treatment


title: Organoid cells, HER2 and PIK3CA Mutation, HP2


title: glioblastoma stem cells, U3024


title: siLTB4R_3_EXPB

value: EXPB


title: CD8+ T cells 5d activation (H2O) donor 1

tag: individual

value: donor 1

value: Blood

value: CD8+ T cells

tag: time

value: 5d activation


title: glioblastoma stem cells, U3017

value: glioblastoma multiforme

value: glioblastoma stem cells


title: glioblastoma stem cells, U3065


title: Organoid cells, HER2 and PIK3CA Mutation, HP1


title: Organoid cells, HER2 Mutation, H4

value: HER2 Mutation


title: glioblastoma stem cells, G166


title: Astrocytes_#78_Fetal_hTERT_Rep1_P27_Bulk

description:
Sample#78_Astrocytes_Fetal_hTERT_Replicate1_Passage27_Bulk
205103220172_R01C01

tag: name

tag: htert

tag: source age (years)


title: glioblastoma stem cells, U3013

tag: cell type


title: siLTB4R_1_EXPB

tag: tissue

tag: replicate


title: Organoid cells, HER2 Mutation, H3

tag: cell line


title: siHCAR3_3_EXPB


title: Organoid cells, HER2 and PIK3CA Mutation, HP4


title: DN-ets-4_PA_Rep 1

city: Taipei

first: Yi-Ting

last: Tsai

address: No.1 Jen Ai road section 1

country: Taiwan

institute: National Taiwan University

data_processing:
The sequencing data were uploaded to the Galaxy web platform, and we used the public server at usegalaxy.org to analyze the data.Sequencing reads were aligned to the C. elegans genome WS220 (ce10) by using HISAT2 (v 2.2.1). Aligned transcripts were first quantified e by featureCounts (V 2.0.1) f0ollow by DESeq2 (v 2.11.40.7) to obtain differential expressed genes (adjusted p value < 0.05).
Assembly: WS220(ce10)
Supplementary files format and content: All normalize counts measurements from Deseq2

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: worms were synchronized by bleach prep. Collected eggs were dropped onto agar plates seeded with OP50 and grown at 20 degrees C until the L4 larval stage.

extract_protocol:
The total RNA used for  mRNAseq preparation was extracted from 100 25°C-grown 2-day-old adult worms by TRIzol reagent (Invitrogen).
Libraries were constructed using KAPA mRNA HyperPrep Kit (Roche) and KAPA Dual-Indexed Adapter Kit (Roche) following manufacturer's protocols.

treatment_protocol: L4 animals fed with non-pathogenic (OP50) or pathogenic (PA14) bacteria for 48 hours at 25 degrees and hand pick 100 worms for RNA extraction.

tag: age

value: day 2

value: whole animal


title: ets-4_PA_Rep 2


title: glioblastoma stem cells, G144


title: siCon_6_EXPB

value: siCon


title: ets-4_PA_Rep 1


title: glioblastoma stem cells, G26


title: Organoid cells, HER2 Mutation, H2

value: tumor breast


title: Organoid cells, HER2 Mutation, H1

value: Organoid cells


title: DN_PA_Rep 2


title: siCon_5_EXPB


title: glioblastoma stem cells, G14


title: glioblastoma stem cells, G7


title: DN_PA_Rep 1


title: Organoid cells, PIK3CA Mutation, P4

value: PIK3CA Mutation


title: U3013, day 38, rep 2

data_processing:
Sequencing reads were mapped against the custom sgRNA library ("Human_Epi_gRNA_library.txt") with bowtie (v1.2.2) using parameter -m 1 -v 1.
Assembly: custom: Human_Epi_gRNA_library.txt
Supplementary files format and content: tab-delimited text files including sgRNA name (sgRNA) and raw mapped counts for each cell line replicate and timepoint
Supplementary files format and content: tab-delimited text file of custom sgRNA library containing sgRNA name and sequence used for mapping (Human_Epi_gRNA_library.txt)

extract_protocol:
Genomic DNA was extracted using DNeasy Blood & Tissue kit (Qiagen).
A two-step PCR procedure was employed using KAPA HiFi HotStart polymerase (KAPA) to amplify sgRNA sequences from genomic DNA and to incorporate add Illumina adapters and multiplexing barcodes to sgRNA amplicons. Purified PCR products were quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher) and KAPA Library Quantification Kit (Roche), pooled in equimolar quantities and sequenced on a NextSeq 500 instrument using a single-end 75bp kit (Illumina).
OTHER: CRISPR screen

treatment_protocol: The domain-focused epigenetic sgRNA library was used in lentiviral pooled format to transduce Cas9-BSD expressing glioma stem cell lines (G166 and U3013) at ∼500-fold representation of the library at an MOI of 0.3. Two days after transduction, 1–2 μg/ml puromycin was added for 5 days. A portion of cells was harvested as day 0 time point after selection was completed. The rest of the cells were then passaged to maintain 500-fold representation and cultured for an additional 35–38 days (eight to ten cell doublings). During the screening period antibiotic selection for Cas9 and sgRNA expression was maintained at 2.5 μg/ml blasticidine and 0.5 μg/ml puromycin, respectively.

value: CRISPR/Cas9 knockout screen

value: day 38


title: DN-ets-4_PA_Rep 2


title: LongHS_3, 40.5°C  for 3 days

city: Rehovot

first: Sharon

last: Schlesinger

address: Herzl 229

department: Animal Science

country: Israel

institute: Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem

data_processing:
Sequence reads were trimmed for adaptor and polyA using Cutadapt
Trimmed sequence reads were mapped to Bos_taurus.ARS-UCD1.2 genome using STAR
Read count extraction to fatures using HTSeq
Normalization of the counts and differential expression analysis using DESeq
Assembly: Bos_taurus.ARS-UCD1.2

organism: Bos taurus

source_name: umbilical cord

growth_protocol: mesenchymal cells were maintained in low glucose Dulbecco's Modified Eagle's Medium, containing 10% Fetal Bovine Serum (FBS), penicillin-streptomycin solution 1% , Glutamine 1%, in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted via PureLink RNA Minikit
Library preparation was done using the INCPM mRNA library of the Weizmann Institute, Rehovot.

treatment_protocol: mesenchymal cells were maintained in low glucose Dulbecco's Modified Eagle's Medium, containing 10% Fetal Bovine Serum (FBS), penicillin-streptomycin solution 1% , Glutamine 1%, in humidified atmosphere with 5% CO2 at 40.5C

value: umbilical cord

value: primary cell culture

value: mesenchymal stem cells

tag: group

value: LongHS

value: LongHS_3, 40.5C  for 3 days


title: siLTB4R_2_EXPB

value: Primary neonatal pooled human keratinocytes

value: skin

value: EXPB


title: Organoid cells, PIK3CA Mutation, P3

tag: genotype


title: N2_PA_Rep 2


title: Organoid cells, PIK3CA Mutation, P2


title: N2_PA_Rep 1


title: U3013, day 38, rep 1

value: glioblastoma multiforme

value: glioblastoma stem cells


title: ShortNT_3, 37°C  for 6 hours

value: ShortNT

value: ShortNT_3, 37C  for 6 hours


title: Organoid cells, PIK3CA Mutation, P1

value: tumor breast


title: U3013, day 0, rep 2

value: day 0


title: DN-ets-4_OP_Rep 2

value: day 2

value: whole animal


title: Organoid cells, WT, WT3

source_name: normal breast

value: normal breast

value: Organoid cells

value: WT


title: LongHS_2, 40.5°C  for 3 days

value: umbilical cord

value: primary cell culture

value: mesenchymal stem cells

value: LongHS_2, 40.5C  for 3 days


title: DN-ets-4_OP_Rep 1


title: ShortHS_Recovery_2, 40.5°C  for 6 hours, 37°C for 66 hours

value: ShortHS_Recovery_2, 40.5C  for 6 hours, 37C for 66 hours


title: Organoid cells, WT, WT2


title: G166, day 35, rep 2

value: CRISPR/Cas9 knockout screen

value: day 35


title: ets-4_OP_Rep 3


title: LongNT_2, 37°C  for 3 days

value: LongNT

value: LongNT_2, 37C  for 3 days


title: Organoid cells, WT, WT1


title: G166, day 35, rep 1

value: glioblastoma multiforme

value: glioblastoma stem cells


title: ets-4_OP_Rep 2


title: U14_oeF3

city: Shenzhen

first: sheng

last: zhong

address: The Xinhu Road 1333

country: China

institute: The Sourthern Medical University

data_processing:
Raw data (raw reads) were processed using Trimmomatic . The reads  containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the  clean reads were mapped to reference genome using hisat2
DEGs were identified using the DESeq  functions estimateSizeFactors and nbinomTest. P value < 0.05 and
foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression
Assembly: hg19
Supplementary files format and content: tab-delimited text files include fold  enrichment for each Sample

source_name: cervical

extract_protocol:
The experimental flow of transcriptome sequencing  Enrichment of eukaryotes with magnetic beads with Oligo(dT) after extraction of sample total RNA and digestion of DNA with DNase  mRNA (in the case of prokaryotes, mRNA is enriched by removing rRNA with the kit);
After passing the Agilent 2100 Bioanalyzer QC, use the Wumina HiSeqTM 2500 or Illumina HiSeq X  Ten other sequencers were sequenced, yielding 125bp or 150bp paired-end data.

value: cervical

value: overexpression


title: ShortHS_2, 40.5°C  for 6 hours

value: ShortHS

value: ShortHS_2, 40.5C  for 6 hours


title: ShortHS_3, 40.5°C  for 6 hours

value: ShortHS_3, 40.5C  for 6 hours


title: ShortNT_2, 37°C  for 6 hours

value: ShortNT

value: ShortNT_2, 37C  for 6 hours


title: G166, day 0, rep 1

value: day 0


title: U14_oeF2


title: ets-4_OP_Rep 1

value: day 2

value: whole animal


title: LongHS_1, 40.5°C  for 3 days

value: umbilical cord

value: primary cell culture

value: mesenchymal stem cells

value: LongHS

value: LongHS_1, 40.5C  for 3 days


title: DN_OP-Rep 3


title: U14_oeF


title: ShortHS_Recovery_1, 40.5°C  for 6 hours, 37°C for 66 hours

value: ShortHS_Recovery_1, 40.5C  for 6 hours, 37C for 66 hours


title: DN_OP-Rep 2


title: U14_3

value: WT


title: U3013, day 0, rep 1

value: glioblastoma multiforme

value: glioblastoma stem cells

value: CRISPR/Cas9 knockout screen


title: LongNT_1, 37°C  for 3 days

value: LongNT

value: LongNT_1, 37C  for 3 days


title: DN_OP_Rep 1


title: siCon_4_EXPB

value: Primary neonatal pooled human keratinocytes

value: skin

value: siCon

value: EXPB


title: N2_OP_Rep 2

value: day 2

value: whole animal


title: U14_2

value: cervical


title: ShortHS_1, 40.5°C  for 6 hours

value: umbilical cord

value: primary cell culture

value: mesenchymal stem cells

value: ShortHS

value: ShortHS_1, 40.5C  for 6 hours


title: U14_1

value: WT


title: Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours [POXKu70T_POX09752]

status: Public on Jul 20 2023

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Remove reads with adapters;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more  than 10).
The clean reads mapped onto the genome of P. oxalicum wild type strain HP7-1 to functional annotation, susing the software BWA v0.7.10-r789 and Bowtie2 v2.1.0.
FPKM, representing gene expression levels, was calculated with the software RSEM v1.2.12
DEGs were screened with NOISeq or DESeq2 tools
Genome_build: GenBank database under accession number JRVD00000000
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Penicillium oxalicum

source_name: Mycelium

growth_protocol: Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.

extract_protocol: Total RNA were extracted using TRIzol RNA Kit

tag: strain


title: G166, day 0, rep 2

value: glioblastoma multiforme

value: glioblastoma stem cells

value: day 0


title: Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours [POXKu70S_POX09752]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours [POXKu70F_POX09752]


title: Mycelium of 1 gram Mutant POX09752 were cultured in 2% Avicel liquid medium for 24 hours [MuPOX09752T]


title: Mycelium of 1 gram Mutant POX09752 were cultured in 2% Avicel liquid medium for 24 hours [MuPOX09752F]


title: Mycelium of 1 gram Mutant POX09752 were cultured in 2% Avicel liquid medium for 24 hours [MuPOX09752S]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours [OE7071_Ku70F_POX07071]

data_processing:
Remove reads with adapters;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more  than 10).
The clean reads mapped onto the genome of P. oxalicum wild type strain HP7-1 to functional annotation, susing the software BWA v0.7.10-r789 and Bowtie2 v2.1.0.
FPKM, representing gene expression levels, was calculated with the software RSEM v1.2.12
DEGs were screened with NOISeq or DESeq2 tools
Genome_build: GenBank database under accession number JRVD00000000
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.


title: Mycelium of 1 gram overexpression strain POX07071 were cultured in 2% Avicel liquid medium for 24 hours [OE7071T]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours [OE7071_Ku70T_POX07071]


title: Mycelium of 1 gram overexpression strain POX07071 were cultured in 2% Avicel liquid medium for 24 hours [OE7071F]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours [POXKu70S]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours [POXKu70T]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours [POXKu70F]


title: male_WT

type: RNA

city: Kobe

first: Akari

last: Inada

state: Hyogo

address: 6‑3‑7 Minatojima　Minamimachi

department: Institute of Biomedical Research and Innovation (IBRI)

country: Japan

institute: Foundation for Biomedical Research and Innovation at Kobe (FBRI)

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: islet, male wild-type

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Mouse islets were freshly isolated via four steps as follows: pancreatic perfusion (inserting a cannula into the common bile duct and perfusing the pancreas with cold Hank’s balanced salt solution containing collagenase, digestion of the pancreas, separation on Histopaque-1077 and 1119 gradients, and washing. Then, high-quality islets were handpicked using a Stemi 2000 stereomicroscope.

tag: Sex

value: male

value: islet


title: female_Tg

source_name: islet, female Tg

value: female


title: male_Tg

source_name: islet, male Tg diabetic


title: Mycelium of 1 gram Mutant POX07071 were cultured in 2% Avicel liquid medium for 24 hours [MuPOX07071T]


title: Mycelium of 1 gram Mutant POX07071 were cultured in 2% Avicel liquid medium for 24 hours [MuPOX07071F]


title: N2_OP_Rep 1


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours[POXKu70S_POX06509]

extract_protocol:
Total RNA were extracted using TRIzol RNA Kit
A cDNA library with 100 bp of length was constructed using the extracted total RNA, and assessed with the ABI StepOnePlus Real-Time PCR System and the Agilent 2100 Bioanalyzer. The eligible cDNA library was sequenced via the Illumina HiSeq 4000 system


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours[POXKu70F_POX06509]


title: ShortNT_1, 37°C  for 6 hours

value: ShortNT

value: ShortNT_1, 37C  for 6 hours


title: Mycelium of 1 gram Mutant POX06509 were cultured in 1% AVicel liquid medium for 24 hours[MuPOX06509T]


title: male_Tg_E_only

description: gene expression after 6 wks of implantation

source_name: islet, male Tg-E2-implanted


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours [POXKu70T_POX05503]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours[POXKu70T_POX06509]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours [POXKu70F_POX05503]


title: Mycelium of 1 gram Mutant POX06509 were cultured in 1% AVicel liquid medium for 24 hours[MuPOX06509S]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours [POXKu70S_POX05503]


title: Mycelium of 1 gram Mutant POX06509 were cultured in 1% AVicel liquid medium for 24 hours[MuPOX06509F]


title: Mycelium of 1 gram Mutant POX05503 were cultured in 1% AVicel liquid medium for 24 hours [MuPOX05503T]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 2% Avicel liquid medium for 24 hours [OE7071_Ku70S_POX07071]


title: Mycelium of 1 gram Mutant POX05503 were cultured in 1% AVicel liquid medium for 24 hours [MuPOX05503S]


title: Mycelium of 1 gram Mutant POX05503 were cultured in 1% AVicel liquid medium for 24 hours [MuPOX05503F]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours [POXKu70T_POX01907]


title: Mycelium of 1 gram Mutant POX08340 were cultured in 1% starch liquid medium for 24 hours [MuPOX08340T]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours [POXKu70F_POX01907]


title: Mycelium of 1 gram Mutant POX08340 were cultured in 1% starch liquid medium for 24 hours [MuPOX08340S]


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours [POXKu70S_POX01907]


title: Mycelium of 1 gram Mutant POX08340 were cultured in 1% starch liquid medium for 24 hours [MuPOX08340F]


title: Mycelium of 1 gram Mutant POX01907 were cultured in 1% starch liquid medium for 24 hours [MuPOX01907S]


title: Mycelium of 1 gram Mutant POX01907 were cultured in 1% starch liquid medium for 24 hours [MuPOX01907T]


title: Mycelium of 1 gram Mutant POX01907 were cultured in 1% starch liquid medium for 24 hours [MuPOX01907F]


title: D14_TE_1_ATACseq

city: Gainesville

first: Zongliang

last: Jiang

state: Florida

address: 2033 Mowry Rd, Cancer & Genetics Research Bldg, Room 303

department: Dept. of Animal Sciences

institute: University of Florida

data_processing:
All quality assessed ATAC-seq reads were aligned to the bovine reference genome using Bowtie 2.3 with following options: –very-sensitive -X 2000 –no-mixed –no-discordant. Alignments resulted from PCR duplicates or locations in mitochondria were excluded. Only unique alignments within each sample were retained for subsequent analysis. ATAC-seq peaks were called separately for each sample by MACS2 with following options: –keep-dup all –nolambda –nomodel. The ATAC-seq bigwig files were generated using bamcoverage from deeptools. The ATAC-seq signals were visualised in the Integrative Genome Viewer genome browser. The enrichment of transcriptional factor motifs in peaks was evaluated using HOMER (http://homer.ucsd.edu/homer/motif/). For downstream analysis, we normalised the read counts by computing counts scaled by the number of sequenced fragments multiplied by one million (CPM).
Assembly: ARS-UCD1.2
Supplementary files format and content: peaks

source_name: Embryonic cells

extract_protocol: Not provided

value: trophectoderm (TE)

tag: timepoint


title: D7_TE_3_ATACseq


title: D7_TE_2_ATACseq


title: D14_TE_3_ATACseq


title: D14_TE_2_ATACseq


title: D7_TE_1_ATACseq


title: bTSC_1_ATACseq

value: trophoblast stem cells (TSCs)


title: bTSC_3_ATACseq


title: BNC_D4_3_ATACseq

value: differentiated trophoblast stem cells (TSCs)


title: BNC_D4_2_ATACseq


title: BNC_D4_1_ATACseq


title: bTSC_2_ATACseq


title: p21mTertCD_18M_Rep1_ssRNAseq

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

description: 10X Genomics

data_processing:
Raw sequences are demultiplexed and reads are mapped onto the mm10 reference genome using the v2.3 Cell Ranger pipeline (10X Genomics) to generate a count matrix.7z for each sample.
Assembly: mm10
Supplementary files format and content: matrix table with filtered gene counts for every gene and every sample

source_name: Lung

extract_protocol:
Mouse trachea is injected with 1,5 ml dispase 50 U/ml followed by 0,5 ml agarose 1%. Lung is resected and minced in 3 ml DPBS 1x CaCl2+ and MgCl2. Collagenase/dispase 100 mg/ml is added to the chopped tissue and placed on a rotator at 37 °C for 30 min. Enzymatic activity is inhibited by adding 5 ml of DPBS containing 10% FBS and 1mM EDTA. Cell suspension is filtered through 100 μm nylon cell strainer, treated by DNase I and filtered again through a 40 μm nylon cell strainer. Red blood cells are removed by red blood cell lysis treatment for 90s at room temperature. Finally, lung cells are centrifuged at 150g, 4 °C for 6 min, resuspended in DPBS 1x containing 0,02% BSA and counted.
Single-cell 3’-RNA-Seq samples were prepared using single cell V2 reagent kit and loaded in the Chromium controller according to standard manufacturer protocol (10x Genomics)

value: Lung

tag: genotype/variation

value: p21 mTertCD (+/mTertCD)

value: 18 month-old


title: p21mTertCD_18M_Rep2_ssRNAseq

description: 10X Genomics


title: p21Het_18M_Rep3_ssRNAseq

description: 10X Genomics

value: p21 heterozygotes (+/-)


title: p21mTert_18M_Rep5_ssRNAseq

description: 10X Genomics

value: p21 mTert (+/mTert)


title: p21mTert_18M_Rep4_ssRNAseq

description: 10X Genomics


title: p21mTert_18M_Rep3_ssRNAseq

description: 10X Genomics


title: p21Het_18M_Rep2_ssRNAseq

description: 10X Genomics


title: 9Kb_M_3002

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 9Kb_M_2997


title: 9Kb_M_2999


title: 9Kb_M_3000


title: 9Kb_M_2998


title: 9Kb_M_3003


title: 9Kb_M_2995


title: 9Kb_M_2994


title: Mycelium of 1 gram overexpression strain POX07071 were cultured in 2% Avicel liquid medium for 24 hours [OE7071S]


title: 9Kb_M_2990


title: 9Kb_M_2989


title: 9Kb_M_2980


title: 9Kb_M_2988


title: 9Kb_M_2992


title: 9Kb_M_2981


title: 9Kb_M_2982


title: 9Kb_M_2979


title: 9Kb_M_2978


title: 9Kb_M_2993


title: 9Kb_M_2984


title: 9Kb_M_2977


title: 9Kb_M_2986


title: 9Kb_M_2975


title: 9Kb_M_2976


title: 9Kb_M_3001


title: 9Kb_M_2974


title: 9Kb_M_2973


title: p21mTert_18M_Rep2_ssRNAseq

description: 10X Genomics


title: 9Kb_M_2996


title: 9Kb_M_2970


title: 9Kb_M_2972


title: 9Kb_M_2968


title: 9Kb_M_2969


title: 9Kb_M_2966


title: 9Kb_M_2965


title: 9Kb_M_2962


title: 9Kb_M_2964


title: 9Kb_M_2963


title: 9Kb_M_2954


title: 9Kb_M_2958


title: 9Kb_M_2955


title: 9Kb_M_2960


title: 9Kb_M_2957


title: 9Kb_M_2961


title: 9Kb_M_2959


title: 9Kb_M_2948


title: 9Kb_M_2952


title: 9Kb_M_2953


title: 9Kb_M_2949


title: 9Kb_M_2956


title: 9Kb_M_2944


title: 9Kb_M_2945


title: 9Kb_M_2951


title: 9Kb_M_2946


title: 9Kb_M_2947


title: 9Kb_M_2971


title: 9Kb_M_2941


title: 9Kb_M_2876


title: 9Kb_M_2875


title: 9Kb_M_2873


title: 9Kb_M_2872


title: 9Kb_M_2871


title: 9Kb_M_2870


title: 9Kb_M_2867


title: 9Kb_M_2864


title: 9Kb_M_2865


title: 9Kb_M_2863


title: 9Kb_M_2862


title: 9Kb_M_2860


title: 9Kb_M_2858


title: 9Kb_M_2861


title: 9Kb_M_2856


title: 9Kb_M_2855


title: 9Kb_M_2854


title: 9Kb_M_2950


title: 9Kb_M_2848


title: 9Kb_M_2852


title: 9Kb_M_2942


title: 9Kb_M_2851


title: 9Kb_M_2849


title: 9Kb_M_2853


title: 9Kb_M_2846


title: 9Kb_M_2845


title: 9Kb_M_2868


title: 9Kb_M_2844


title: 9Kb_M_2859


title: 9Kb_M_2857


title: 9Kb_M_2866


title: 9Kb_M_2843


title: 9Kb_M_2840


title: 9Kb_M_2839


title: 9Kb_M_2841


title: 9Kb_M_2838


title: 9Kb_M_2837


title: 9Kb_M_2836


title: 9Kb_M_2835


title: 9Kb_M_2832


title: 9Kb_M_2847


title: 9Kb_M_2828


title: 9Kb_M_2830


title: 9Kb_M_2831


title: 9Kb_M_2829


title: 9Kb_M_2826


title: 9Kb_M_2827


title: 9Kb_M_2842


title: 9Kb_M_2824


title: 9Kb_M_2822


title: 9Kb_M_2823


title: 9Kb_M_2825


title: 9Kb_M_2820


title: 9Kb_M_2819


title: 9Kb_M_2821


title: 9Kb_M_2833


title: 9Kb_M_2818


title: 9Kb_M_2817


title: 9Kb_M_2811


title: 9Kb_M_2814


title: 9Kb_M_2812


title: 9Kb_M_2813


title: 9Kb_M_2815


title: 9Kb_M_2810


title: 9Kb_M_2809


title: Mycelium of 1 gram Mutant POX07071 were cultured in 2% Avicel liquid medium for 24 hours [MuPOX07071S]


title: 9Kb_M_2807


title: 9Kb_M_2806


title: 9Kb_M_2808


title: 9Kb_M_2805


title: 9Kb_M_2803


title: 9Kb_M_2804


title: 9Kb_M_2802


title: 9Kb_M_2801


title: 9Kb_M_2798


title: 9Kb_M_2816


title: 9Kb_M_2800


title: 9Kb_M_2795


title: 9Kb_M_2794


title: 9Kb_M_2796


title: 9Kb_M_2797


title: 9Kb_M_2792


title: 9Kb_M_2791


title: 9Kb_M_2788


title: 9Kb_M_2793


title: 9Kb_M_2790


title: 9Kb_M_2789


title: 9Kb_M_2787


title: 9Kb_M_2785


title: 9Kb_M_2784


title: 9Kb_M_2783


title: 9Kb_M_2780


title: 9Kb_M_2782


title: 9Kb_M_2779


title: 9Kb_M_2778


title: 9Kb_M_2776


title: 9Kb_M_2775


title: 9Kb_M_2773


title: 9Kb_M_2771


title: 9Kb_M_2774


title: 9Kb_M_2772


title: 9Kb_M_2770


title: 9Kb_M_2786


title: 9Kb_M_2769


title: 9Kb_M_2768


title: 9Kb_M_2781


title: 9Kb_M_2763


title: 9Kb_M_2764


title: 9Kb_M_2761


title: 9Kb_M_2760


title: 9Kb_M_2758


title: 9Kb_M_2756


title: 9Kb_M_2754


title: 9Kb_M_2755


title: 9Kb_M_2753


title: 9Kb_M_2752


title: 9Kb_M_2750


title: 9Kb_M_2557


title: 9Kb_M_2556


title: 9Kb_M_2767


title: 9Kb_M_2552


title: 9Kb_M_2555


title: 9Kb_M_2554


title: 9Kb_M_2551


title: 9Kb_M_2553


title: 9Kb_M_2550


title: 9Kb_M_2765


title: 9Kb_M_2759


title: 9Kb_M_2549


title: 9Kb_M_2766


title: 9Kb_M_2548


title: 9Kb_M_2547


title: 9Kb_M_2544


title: 9Kb_M_2751


title: 9Kb_M_2543


title: 9Kb_M_2538


title: 9Kb_M_2540


title: 9Kb_M_2542


title: 9Kb_M_2546


title: 9Kb_M_2539


title: 9Kb_M_2545


title: 9Kb_M_2541


title: 9Kb_M_2536


title: 9Kb_M_2534


title: 9Kb_M_2532


title: 9Kb_M_2535


title: 9Kb_M_2533


title: 9Kb_M_2529


title: 9Kb_M_2530


title: 9Kb_M_2528


title: 9Kb_M_2525


title: 9Kb_M_2834


title: 9Kb_M_2524


title: 9Kb_M_2526


title: 9Kb_M_2527


title: 9Kb_M_2874


title: 9Kb_M_2522


title: 9Kb_M_2523


title: 9Kb_M_2520


title: 9Kb_M_2518


title: 9Kb_M_2519


title: 9Kb_M_2515


title: 9Kb_M_2516


title: 9Kb_M_2514


title: 9Kb_M_2537


title: 9Kb_M_2512


title: 9Kb_M_2513


title: 9Kb_M_2869


title: 9Kb_M_2511


title: 9Kb_M_2531


title: 9Kb_M_2510


title: 9Kb_M_2507


title: 9Kb_M_2508


title: 9Kb_M_2850


title: 9Kb_M_2506


title: 9Kb_M_2505


title: 9Kb_M_2521


title: 9Kb_M_2504


title: 9Kb_M_2501


title: 9Kb_M_2517


title: 9Kb_M_2500


title: 9Kb_M_2502


title: 9Kb_M_2498


title: 9Kb_M_2497


title: 9Kb_M_2503


title: 9Kb_M_2496


title: 9Kb_M_2495


title: 9Kb_M_2238


title: 9Kb_M_2494


title: 9Kb_M_2236


title: 9Kb_M_2234


title: 9Kb_M_2233


title: 9Kb_M_2509


title: 9Kb_M_2231


title: 9Kb_M_2232


title: 9Kb_M_2499


title: 9Kb_M_2235


title: 9Kb_M_2230


title: 9Kb_M_2229


title: 9Kb_M_2228


title: 9Kb_M_2227


title: 9Kb_M_2224


title: 9Kb_M_2226


title: 9Kb_M_2223


title: 9Kb_M_2221


title: 9Kb_M_2222


title: 9Kb_M_2217


title: 9Kb_M_2220


title: 9Kb_M_2218


title: 9Kb_M_2216


title: 9Kb_M_2219


title: 9Kb_M_2214


title: 9Kb_M_2215


title: 9Kb_M_2237


title: 9Kb_M_2213


title: 9Kb_M_2209


title: 9Kb_M_2212


title: 9Kb_M_2210


title: 9Kb_M_2208


title: 9Kb_M_2207


title: 9Kb_M_2205


title: 9Kb_M_2206


title: 9Kb_M_2203


title: 9Kb_M_2225


title: 9Kb_M_2200


title: 9Kb_M_2201


title: 9Kb_M_2204


title: 9Kb_M_2202


title: 9Kb_M_2199


title: 9Kb_M_2198


title: 9Kb_M_2196


title: 9Kb_M_2195


title: 9Kb_M_2197


title: 9Kb_M_2194


title: 9Kb_M_2193


title: 9Kb_M_2211


title: 9Kb_M_2187


title: 9Kb_M_2186


title: 9Kb_M_2191


title: 9Kb_M_2185


title: 9Kb_M_2188


title: 9Kb_M_2189


title: 9Kb_M_2190


title: 9Kb_M_2183


title: 9Kb_M_2192


title: 9Kb_M_2184


title: 9Kb_M_2181


title: 9Kb_M_2178


title: 9Kb_M_2180


title: 9Kb_M_2177


title: 9Kb_M_2182


title: 9Kb_M_2174


title: 9Kb_M_2175


title: 9Kb_M_2173


title: 9Kb_M_2176


title: 9Kb_M_2179


title: 9Kb_M_2168


title: 9Kb_M_2167


title: 9Kb_M_2166


title: 9Kb_M_2170


title: 9Kb_M_2169


title: 9Kb_M_2165


title: 9Kb_M_2164


title: 9Kb_M_2163


title: 9Kb_M_2161


title: 9Kb_M_2158


title: 9Kb_M_2160


title: 9Kb_M_2159


title: 9Kb_M_2162


title: 9Kb_M_2155


title: 9Kb_M_2154


title: 9Kb_M_2156


title: 9Kb_M_2153


title: 9Kb_M_2172


title: 9Kb_M_2171


title: 9Kb_M_2150


title: 9Kb_M_2149


title: 9Kb_M_2151


title: 9Kb_M_2147


title: 9Kb_M_2145


title: 9Kb_M_2146


title: 9Kb_M_2144


title: 9Kb_M_2138


title: 9Kb_M_2142


title: 9Kb_M_2148


title: 9Kb_M_2139


title: 9Kb_M_2140


title: 9Kb_M_2141


title: 9Kb_M_2136


title: 9Kb_M_2137


title: 9Kb_M_2135


title: 9Kb_M_2157


title: 9Kb_M_2152


title: 9Kb_M_2133


title: 9Kb_M_2131


title: 9Kb_M_2134


title: 9Kb_M_2130


title: 9Kb_M_2129


title: 9Kb_M_2128


title: 9Kb_M_2125


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title: 9Kb_M_2123


title: 9Kb_M_2122


title: 9Kb_M_2143


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title: 9Kb_M_2111


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title: 9Kb_M_1913


title: 9Kb_M_1911


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title: 9Kb_M_1908


title: 9Kb_M_1907


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title: 9Kb_M_1789


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title: 9Kb_M_1783


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