title: Slide-344-05-26-22-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 650
DSP-1001660010694-A-D06


title: Phgdhfl/fl Cx3cr1-Cre, TEM, rep2

status: Public on Jan 27 2024

type: SRA

city: Vienna

first: Wolfram

last: Weckwerth

address: Djerassiplatz 1

country: Austria

institute: University of Vienna

library_source: transcriptomic

data_processing:
The raw reads in fastq format were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat2
Fragments per kilobase of transcript per million fragments mapped (FPKM) was calculated by using HT-seq v0.6
The identified transcripts are further assembled and analyzed for differential analysis with the DESeq2.
Genes with low counts greater than 10
adjusted p-value less than 0.05
Assembly: mm10
Supplementary files format and content: Normalized FPKM values for each sample (tab-delimited text file)

molecule: total RNA

organism: Mus musculus

source_name: BMDMS

growth_protocol: Phgdhfl/fl Cx3cr1-Cre and Phgdhfl/fl BMDMs were seeded in a 6-well plate at a density of 1 × 10^6 cells per well and allowed to adhere overnight

extract_protocol:
Total RNA was isolated using the TRl reagent
The NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used for preparing the sequencing libraries

treatment_protocol: Then the media were replaced with AE17-TCM and incubated for 24 hours

tag: cell line

value: BMDMS

tag: cell type

value: Macrophage

tag: genotype

value: macrophage-specific Phgdh KO


title: Slide-344-05-26-22-002-Non-epi

city: Pittsburgh

first: Ayah

middle: N.

last: Al-Bzour

state: Pennsylvania

address: Pittsburgh

department: Department of Medicine, Division of Hematology & Oncology

country: USA

institute: University of Pittsburgh Medical Center (UPMC)

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 649
DSP-1001660010694-A-D05

data_processing:
*library strategy: GeoMx DSP (RNA-seq)
Illumina FASTQ sequencing files were processed using the GeoMx NGS Pipeline version 2.3.3.10 to generate digital count conversion (DCC) files which were subsequently analyzed using the GeoMx DSP Analysis Suite version 2.4.1 to perform data QC and Q3 normalization using all target groups
Assembly: GeoMx Cancer Transcriptome Atlas
Supplementary files format and content: Processed data files are provided in DCC format

organism: Homo sapiens

source_name: Stroma

extract_protocol:
Spatial profiling was performed on three regions of interests (ROIs) from formalin fixed paraffin embedded tissue (FFPE) sections for each patient sample. Tumor epithelial compartment (highlighted by pan-cytokeratin, green-fluorescent marker) and the stroma compartment (pan-cytokeratin negative).
This involved library preparation and assessing the quality and quantity of the purified library using Agilent Bioanalyzer and Qubit assays, respectively. NGS libraries were sequenced using the Illumina NextSeq 550 instrument

tag: tissue

value: Stroma


title: Muscle_SMAD4_iKO_replicate4

city: Durham

first: Yarui

last: Diao

state: North Carolina

address: 307 Research Drive, Box 3709

department: Cell Biology

institute: Duke University School of Medicine

data_processing:
Read alignment with STAR v2.7.5c
Feature counts and creation of count matrix using Cufflinks v2.2.2, downstream anlysis using DESEQ2
Assembly: mm10
Supplementary files format and content: Tab-separated FPKM-normalized gene counts for each sample

molecule: polyA RNA

source_name: Mouse Muscle

extract_protocol:
40 h after the CTX injury, MuSCs were isolated from the digested gaskin muscles using FACS and then underwent RNA extraction using the NucleoSpin RNA XS kit from Macherey-Nagel
Smart Seq

treatment_protocol: Treated with cardiotoxin

value: Mouse Muscle

value: Skeletal Muscle Satellite Cells

value: Smad4 f/f:Pax7 CreER/CreER :R26 YFP/YFP

tag: treatment

value: Cardiotoxin treatment and Collagenase digestion of tissue


title: Sox4 hepatocytes, 18hpi, rep3

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

library_source: genomic

data_processing:
Reads were aligned to the mouse genome (mm10) using Bowtie2 with options ‘--very-sensitive -X 1000 --dovetail -1’
duplicates were removed using Picard (http://broadinstitute.github.io/picard/).
Assembly: mm10
Supplementary files format and content: The bigwig files (.bw) are generated by aligning the sequence tags to mm10 by bowtie2 with default parameters and converting the bam files to bigwig using bamCoverage by RPGC normalization.
Supplementary files format and content: Peak calling was performed using MACS2 with the options ‘--nomodel --extsize 200 --shift -100’.

molecule: genomic DNA

source_name: Liver

extract_protocol:
Nuclei were isolated from sorted cells using a solution of 10 mM Tris-HCl pH 7.4/10 mM NaCl/3 mM MgCl2/0.1% IGEPAL CA-630.
Immediately following isolation, the transposition reaction was conducted using Tn5 transposase and TD buffer (Illumina) for 30 minutes at 37 °C.
Transposed DNA fragments were purified using a Qiagen MinElute Kit, barcoded, and PCR amplified for xx cycles using NEBNext High Fidelity 2x PCR master mix (New England Biolabs), and then the libraries were purified with AMPure XP beads.

treatment_protocol: AAV8-TBG-Cre (EV) or AAV8-TBG-HA-Sox4-P2A-Cre (Sox4) were retro-orbitally injected. 4 days post injection, hepatocytes were harvsted.

value: Liver

value: Hepatocyte

value: AAV8-TBG-HA-Sox4-P2A-Cre injected; harvested 18 hours post injection


title: Phgdhfl/fl, TEM, rep3

value: WT


title: Phgdhfl/fl Cx3cr1-Cre, TEM, rep1


title: Sox4 hepatocytes, 18hpi, rep1


title: Slide-344-05-26-22-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 646
DSP-1001660010694-A-D02

source_name: Tumor

value: Tumor


title: Slide-344-05-26-22-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 647
DSP-1001660010694-A-D03


title: C2G1Res1_R6

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description:
67_Wt_PS_susceptible_2
Gene-wise_read_countings.csv

data_processing:
reads were mapped to the Mus musculus GRCm38.p5 genome using STAR (Dobin et al. 2013)
the reads per position were determined using HTSeq (Anders et al. 2015)
statistics were performed using the DeSeq2 R package (Love et al. 2014)
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Gene wise read countings in tabular separated plain text format

source_name: hippocampus

extract_protocol:
brains were extracted, snapfrozen in isopentane, subsequently the hippocampus was dissected, hippocampi of both hemispheres were poderised at - 80 ͦC, blended and split in two equal portions. RNA was extracted from one portion, using a combination of the classical phenol-chloroform (QIAZOL) method and the column-based protocol of the commercial miRNeasy Mini kit (Qiagen, Hilden, Germany) for fatty tissue.
library preparation was performed by IGA Technologies (Undine, Italy)

treatment_protocol: dams were exposed to restraint stress three times per day from embryonic day 13 to emrbionic day 17; adult female offspring were investigated

tag: strain

value: hippocampus

tag: age

value: 3 months

tag: condition

value: PS-susceptible


title: Slide-343-05-26-22-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 653
DSP-1001660010694-A-D09


title: Phgdhfl/fl, TEM, rep2


title: Slide-344-05-26-22-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 648
DSP-1001660010694-A-D04


title: C2G1Res1_R7

description:
84_Wt_PS_susceptible_2
Gene-wise_read_countings.csv


title: Phgdhfl/fl, TEM, rep4


title: C2G1Res1_R5

description:
60_Wt_PS_susceptible_2
Gene-wise_read_countings.csv


title: Slide-321-05-26-22-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 645
DSP-1001660010694-A-C10


title: SS3, Sham surgery-rep3

city: Beijing

first: shuang

middle: qing

last: wei

address: No. 11, Bei San Huan Dong Lu, Chaoyang District

country: China

institute: beijing university of chinese medcine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
STAR software was used for mapping and alignment;version:2.7.0; parameters:for i in $(cat $name);do;echo "$i";#mkdir ./"$i";STAR --genomeDir $index \  --runThreadN 20 \  --readFilesIn ./"$i"/"$i"_1.fq.gz ./"$i"/"$i"_2.fq.gz \  --readFilesCommand zcat \  --outFileNamePrefix ./"$i"/"$i"_ \  --outSAMtype BAM Unsorted SortedByCoordinate \  --quantMode GeneCounts ;done
Genome_build: gencode.vM24.primary_assembly.annotation
Supplementary_files_format_and_content: tab-delimited text files includeraw gene counts for each Sample

source_name: intestine tissue

extract_protocol:
Intestine were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Novaseq 6000 PE Cluster Kit (Illumia) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: intestine

value: Sham surgery


title: Phgdhfl/fl, TEM, rep1

value: BMDMS

value: Macrophage


title: SS4, Sham surgery-rep4


title: C2G1Res1_R8

description:
86_Wt_PS_susceptible_2
Gene-wise_read_countings.csv


title: Slide-321-05-26-22-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 644
DSP-1001660010694-A-C09


title: C2G1Res1_R3

description:
48_Wt_PS_susceptible_2
Gene-wise_read_countings.csv


title: C2G1Res1_R2

description:
44_Wt_PS_susceptible_2
Gene-wise_read_countings.csv


title: C2G1Res1_R1

description:
34_Wt_PS_susceptible_2
Gene-wise_read_countings.csv


title: Slide-321-05-26-22-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 643
DSP-1001660010694-A-C08

value: Stroma


title: SS1, Sham surgery-rep1


title: Slide-321-05-26-22-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 642
DSP-1001660010694-A-C07


title: patient_AML4_untreated

city: Duarte

first: Mariam

last: Murtadha

state: CA

address: 1500 E. Duarte Rd

institute: City of Hope

data_processing:
Sequence reads passing quality check were preprocessed for adaptor and polyA removal using trimmomatic v.0.39 and fastp v.0.23.2
Assembly: mapping to human reference genome hg38 with an index build containing the transcript/gene annotations using STAR v.2.7.9a
Supplementary files format and content: text file

source_name: BM

extract_protocol:
Total RNA was extracted and cleaned with NORGEN Biotek RNA-clean up and concentration kit
Kapa RNA mRNA HyperPrep kit (Kapa Biosystems, Cat KR1352) according to manufacturer's protocol
The final libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit.Sequencing was performed in single read mode of 51-cycle using the Illumina HiSeq 2500 system generating approximately 50 million reads per sample.Real-time analysis (RTA) 2.2.38 software was used to process the image analysis.

value: BM

value: untreated


title: patient_AML4_treated

value: interferon gama, 10 ng/ml


title: Sox4 hepatocytes, 18hpi, rep2


title: C2G1Res1_R4

description:
50_Wt_PS_susceptible_2
Gene-wise_read_countings.csv


title: patient_AML21_treated


title: SEA2, treated by sham electroacupuncture-rep2

value: sham electroacupuncture


title: C2G1Res2_R7

description:
75_Wt_PS_resilient_3
Gene-wise_read_countings.csv

value: PS-resilient


title: patient_AML3_treated


title: C2G1Res2_R8

description:
110_Wt_PS_resilient_3
Gene-wise_read_countings.csv


title: Slide-340-05-26-22-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 639
DSP-1001660010694-A-C04


title: Slide-321-05-26-22-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 641
DSP-1001660010694-A-C06


title: C2G1Res2_R5

description:
57_Wt_PS_resilient_3
Gene-wise_read_countings.csv


title: patient_AML21_untreated


title: IM3, intestinal manipulation model-rep3

value: intestinal manipulation model


title: Slide-321-05-26-22-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 640
DSP-1001660010694-A-C05


title: SEA1, treated by sham electroacupuncture-rep1


title: C2G1Res2_R4

description:
45_Wt_PS_resilient_3
Gene-wise_read_countings.csv


title: patient_AML3_untreated


title: SEA6, treated by sham electroacupuncture-rep6


title: IM1, intestinal manipulation model-rep1


title: Slide-340-05-26-22-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 637
DSP-1001660010694-A-C02


title: Slide-340-05-26-22-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 638
DSP-1001660010694-A-C03


title: Slide-340-05-26-22-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 636
DSP-1001660010694-A-C01


title: ES4, treated by electrical stimulation-rep4

value: electrical stimulation


title: ES2, treated by electrical stimulation-rep2


title: All vestibular neurons, replicate 3

city: New York

first: David

last: Schoppik

state: NY

address: 435 E 30th St

department: Neuroscience Institute

institute: New York University Grossman School of Medicine

library_source: transcriptomic single cell

data_processing:
Cell Ranger v7.0.0
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Hindbrain vestibular neurons

extract_protocol:
Harvested neurons were sorted to isolate single cells, resuspended in L15+2% FBS, and kept on ice until cDNA synthesis
Performed using manufacturer's instructions; 10x Genomics, 3' V3.1

treatment_protocol: Three replicates were untreated. One replicate was photoconverted at 36 hpf to isolate early-born (red, converted Kaede) from late-born (green, unconverted Kaede) neurons.

tag: time

value: 72-74 hours post-fertilization

value: Hindbrain vestibular neurons


title: Slide-340-05-26-22-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 635
DSP-1001660010694-A-B12


title: Early-born vestibular neurons, replicate 1

value: Neurons born before 36 hpf (red photoconverted Kaede)


title: Late-born vestibular neurons, replicate 2

value: Neurons born after 36 hpf (green unconverted Kaede)


title: C2G1Res2_R1

description:
35_Wt_PS_resilient_3
Gene-wise_read_countings.csv

value: hippocampus

value: 3 months


title: C2G1Res2_R6

description:
74_Wt_PS_resilient_3
Gene-wise_read_countings.csv


title: IM2, intestinal manipulation model-rep2

value: intestine


title: ES1, treated by electrical stimulation-rep1


title: All vestibular neurons, replicate 2


title: C1G1Res0_R8

description:
144_Wt_C_C_1
Gene-wise_read_countings.csv

value: no stress


title: C1G1Res0_R7

description:
128_Wt_C_C_1
Gene-wise_read_countings.csv


title: EA5, treated by electroacupuncture-rep5

value: electroacupuncture


title: Slide-330-05-19-2022-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 633
DSP-1001660010694-A-B10

value: Stroma


title: Slide-340-05-26-22-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 634
DSP-1001660010694-A-B11

value: Tumor


title: All vestibular neurons, replicate 1


title: Slide-330-05-19-2022-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 632
DSP-1001660010694-A-B09


title: EA3, treated by electroacupuncture-rep3


title: C1G1Res0_R6

description:
98_Wt_C_C_1
Gene-wise_read_countings.csv


title: EA4, treated by electroacupuncture-rep4


title: Hindbrain vestibular neurons, phox2a-/-, replicate 4

data_processing:
DESeq2
Assembly: GRCz11
Supplementary files format and content: excel file includes raw counts for each sample
Supplementary files format and content: excel file includes normalized counts for each sample

extract_protocol:
RNA was isolated using an RNAqueous Total RNA Isolation Kit. RNA quality and concentration was assessed using an RNA 6000 Pico Kit and a 2100 BioAnalyzer system.
Libraries for bulk RNA sequencing were prepared using the low-input Clontech SMART-Seq HT with Nxt HT kit (Takara)

value: Tg(-6.7Tru.Hcrtr2:GAL4-VP16); Tg(UAS:E1b-Kaede); Tg(isl1:GFP); phox2a-/-


title: C2G1Res2_R3

description:
42_Wt_PS_resilient_3
Gene-wise_read_countings.csv


title: Hindbrain vestibular neurons, siblings, replicate 4

value: Tg(-6.7Tru.Hcrtr2:GAL4-VP16); Tg(UAS:E1b-Kaede); Tg(isl1:GFP); phox2a+/+ or +/-


title: Muscle_Regen_Injured_7days_replicate2

description: Library prep: Tn5 insertion with combinatorial Indexing and size selection

data_processing:
Demultiplexing of cells using an in-house python script, creation of fragment files using Snaptools v1.1
Creation of arrow files and further downstream analyses using ArchR Version 1.0.1 with mostly default parameters
For Arrow files, changed parameters include TSS enrichment cut off of 8 and unique fragment cutoff of 1000 was used.
Assembly: mm10
Supplementary files format and content: Arrow files (in R) containing accessibility matrix and other cell-type-related metadata.

source_name: Skeletal Muscle Hindlimb

extract_protocol:
Dissected tissue, snap frozen, homogenized with gentleMACS
Tn5 insertion with combinatorial Indexing by serial barcode ligation, and size selection

treatment_protocol: Treated with 1.2% barium chloride (wt/vol in H2O)

value: Skeletal Muscle Hindlimb

value: All Muscle cells

value: C57BL6 mice wt

value: BaCl2-treated muscle, snap frozen on dry ice


title: C2G1Res2_R2

description:
39_Wt_PS_resilient_3
Gene-wise_read_countings.csv

value: PS-resilient


title: C1G1Res0_R5

description:
79_Wt_C_C_1
Gene-wise_read_countings.csv


title: C1G1Res0_R4

description:
78_Wt_C_C_1
Gene-wise_read_countings.csv


title: Hindbrain vestibular neurons, phox2a-/-, replicate 3

value: 72-74 hours post-fertilization

value: Hindbrain vestibular neurons


title: Slide-330-05-19-2022-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 631
DSP-1001660010694-A-B08


title: Hindbrain vestibular neurons, siblings, replicate 3


title: Slide-330-05-19-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 629
DSP-1001660010694-A-B06


title: Muscle_Regen_Injured_72hours_replicate2

value: Dissected tissue, snap frozen, homogenized with gentleMACS


title: C1G1Res0_R3

description:
53_Wt_C_C_1
Gene-wise_read_countings.csv

value: hippocampus


title: Slide-330-05-19-2022-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 630
DSP-1001660010694-A-B07


title: Slide-330-05-19-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 628
DSP-1001660010694-A-B05


title: C1G1Res0_R2

description:
23_Wt_C_C_1
Gene-wise_read_countings.csv

value: 3 months


title: Muscle_Regen_Injured_7days_replicate1


title: Hindbrain vestibular neurons, siblings, replicate 2


title: Slide-316-05-19-2022-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 627
DSP-1001660010694-A-B01


title: C1G1Res0_R1

description:
11_Wt_C_C_1
Gene-wise_read_countings.csv


title: Muscle_Regen_Injured_72hours_replicate1


title: Muscle_Regen_Injured_48hours_replicate1


title: Muscle_Regen_Injured_24hours_replicate1


title: IC01-2

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

description: 48 hours after media change, media was collected and spun down at 500g and passed through 0.4 um to remove any cells. 1 ml cell free media was taken for RNA isolation from CM. The rest of the media was used for exosome isolation by adding Polyethylene Glycol 10000 (PEG, HR2-607) to 10 % final and overnight incubation at 4C. The next day PEG/media mixture was spun down at 3000g at 4C for 1 hour. Supernatant was removed. We moved forward with isolating RNA fromthe pellets.

data_processing:
Reads were first collapsed using fastq2collapse, part of the CTK package
UMI extract using umi_tools v1.0.0
Remove polyA linker using cutadapt 2.3
Align to custom fasta file using BWA (0.7.17-r1188)
Sort using samtools v1.7
Deduplicate reads using umi_tools
Count and compare using DESeq2 (1.24)
Supplementary files format and content: count table

source_name: breast cancer cell line

growth_protocol: Cells containing the library were seeded in 10 cm plates. The next day the media was removed and cells were washed with 1X PBS. Cells were then incubated  in media prepared with exosome depleted FBS in standard cell culture conditions for 48 hours.

extract_protocol:
RNA isolation for CM condition was performed using  zymo research Quick-cfRNA Serum & Plasma Kit (cat# R1059). RNA isoltion for EV portion wsa done using Zymo Research Quick-RNA Microprep Kit (cat#R1051)
in-house small RNA library preparation (refer to the methods section)

tag: ev/ic

value: IC


title: Hindbrain vestibular neurons, siblings, replicate 1


title: Hindbrain vestibular neurons, phox2a-/-, replicate 1


title: Slide-316-05-19-2022-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 625
DSP-1001660010694-A-A11


title: Muscle_Regen_Injured_48hours_replicate2


title: C2G2Res1_R6

description:
114_5-Htt+-_PS_susceptible_5
Gene-wise_read_countings.csv

value: PS-susceptible


title: C2G2Res1_R7

description:
121_5-Htt+-_PS_susceptible_5
Gene-wise_read_countings.csv


title: Slide-316-05-19-2022-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 626
DSP-1001660010694-A-A12


title: Slide-316-05-19-2022-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 624
DSP-1001660010694-A-A10


title: Muscle_Regen_Injured_12hours_replicate2

description: Library prep: Tn5 insertion with combinatorial Indexing and size selection


title: Slide-316-05-19-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 623
DSP-1001660010694-A-A09


title: Muscle_Regen_Injured_24hours_replicate2


title: EV01-1

value: EV


title: Slide-316-05-19-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 622
DSP-1001660010694-A-A08


title: IC01-1


title: EV01-2


title: C2G2Res1_R8

description:
122_5-Htt+-_PS_susceptible_5
Gene-wise_read_countings.csv


title: C2G2Res1_R3

description:
87_5-Htt+-_PS_susceptible_5
Gene-wise_read_countings.csv


title: C2G2Res1_R4

description:
103_5-Htt+-_PS_susceptible_5
Gene-wise_read_countings.csv


title: CCM01-2

value: CC


title: Slide-312-05-19-2022-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 621
DSP-1001660010694-A-A05

value: Stroma


title: C2G2Res1_R5

description:
112_5-Htt+-_PS_susceptible_5
Gene-wise_read_countings.csv


title: Slide-312-05-19-2022-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 620
DSP-1001660010694-A-A04

value: Tumor


title: CCM01-1


title: RBM24_exoCLIP

data_processing:
Reads were first collapsed using fastq2collapse, part of the CTK package
UMI extract using umi_tools v1.0.0
Remove polyA linker using cutadapt 2.3
Align to genome using BWA (0.7.17-r1188)
Sort using samtools v1.7
Deduplicate reads using umi_tools
Call peaks using CTK
Assembly: hg38
Supplementary files format and content: BED for peaks

growth_protocol: MDA-MB-231 cells were seeded in 15 cm plates. The next day the media was removed and cells were washed with 1X PBS. Cells were then incubated  in media prepared with exosome depleted FBS in standard cell culture conditions for 48 hours.

extract_protocol:
RNA isolation was done using flag-IP method as described in the method scetion.
Takara Bio SMARTer smRNA-Seq Kit (with some modifications)

treatment_protocol: 48 hours after media change, media was collected and undergone crosslinking 2x at 200 mJ/cm2 254 nm UV. Media was then condensed for the donwstream IP.

value: CM


title: C2G2Res1_R2

description:
73_5-Htt+-_PS_susceptible_5
Gene-wise_read_countings.csv


title: Muscle_Regen_Uninjured_replicate1

value: Skeletal Muscle Hindlimb


title: Muscle_Regen_Injured_6hours

value: All Muscle cells


title: HANRNPB1_exoCLIP


title: Muscle_Regen_Uninjured_replicate2

value: C57BL6 mice wt


title: Slide-342-06-02-2022-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 617
DSP-1001660005138-B-H05


title: Muscle_Regen_Alert_6hours

value: BaCl2-treated muscle, snap frozen on dry ice


title: Muscle_Regen_Alert_12hours


title: HANRNPA2_exoCLIP


title: C2G2Res1_R1

description:
58_5-Htt+-_PS_susceptible_5
Gene-wise_read_countings.csv


title: C2G2Res2_R8

description:
127_5-Htt+-_PS_resilient_6
Gene-wise_read_countings.csv

value: PS-resilient


title: IC02-2

description: 48 hours after media change, media was collected and spun down at 500g and passed through 0.4 um to remove any cells. 1 ml cell free media was taken for RNA isolation from CM. The rest of the media was used for exosome isolation by adding Polyethylene Glycol 10000 (PEG, HR2-607) to 10 % final and overnight incubation at 4C. The next day PEG/media mixture was spun down at 3000g at 4C for 1 hour. Supernatant was removed. We moved forward with isolating RNA fromthe pellets.


title: Slide-342-06-02-2022-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 616
DSP-1001660005138-B-H04


title: WT_8h-3

first: Ana

middle: M

last: Sanchez

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls from Illumina NovaSeq 6000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: DESeq output file

organism: Schizosaccharomyces pombe

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA Seq

tag: growth phase

value: 8 h after transfer to ePMGT(+PO4) medium

tag: growth medium

value: ePMGT(+PO4) medium

value: h-


title: Muscle_Regen_Injured_12hours_replicate1

value: Dissected tissue, snap frozen, homogenized with gentleMACS


title: C2G2Res2_R6

description:
90_5-Htt+-_PS_resilient_6
Gene-wise_read_countings.csv

value: hippocampus

value: 3 months


title: Slide-342-06-02-2022-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 615
DSP-1001660005138-B-H03


title: IC02-1

value: IC


title: WT_8h-2


title: C2G2Res2_R5

description:
89_5-Htt+-_PS_resilient_6
Gene-wise_read_countings.csv


title: Slide-312-05-19-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 619
DSP-1001660010694-A-A03


title: C2G2Res2_R9

description:
134_5-Htt+-_PS_resilient_6
Gene-wise_read_countings.csv


title: WT_8h-1


title: Slide-312-05-19-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 618
DSP-1001660010694-A-A02


title: C2G2Res2_R4

description:
63_5-Htt+-_PS_resilient_6
Gene-wise_read_countings.csv


title: EV02-2

value: EV


title: C2G2Res2_R7

description:
106_5-Htt+-_PS_resilient_6
Gene-wise_read_countings.csv


title: EV02-1


title: Slide-342-06-02-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 613
DSP-1001660005138-B-H01


title: C2G2Res2_R3

description:
29_5-Htt+-_PS_resilient_6
Gene-wise_read_countings.csv


title: Slide-338-06-02-2022-007-Non-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 611
DSP-1001660005138-B-G11


title: WT_4h-3

value: 4 h after transfer to ePMGT(+PO4) medium


title: Slide-342-06-02-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 612
DSP-1001660005138-B-G12


title: WT_4h-2


title: CCM02-1

value: CC


title: C2G2Res2_R2

description:
28_5-Htt+-_PS_resilient_6
Gene-wise_read_countings.csv


title: WT_4h-1


title: Slide-338-06-02-2022-007-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 610
DSP-1001660005138-B-G10

value: Tumor


title: WT_2h-3

value: 2 h after transfer to ePMGT(+PO4) medium


title: IC_RBM24_2

data_processing:
Reads were first collapsed using fastq2collapse, part of the CTK package
UMI extract using umi_tools v1.0.0
Remove polyA linker using cutadapt 2.3
Align to genome using BWA (0.7.17-r1188)
Sort using samtools v1.7
Deduplicate reads using umi_tools
Count and compare using DESeq2 (1.24)
Assembly: hg38
Supplementary files format and content: count table

growth_protocol: Cells  were seeded in 10 cm plates. The next day the media was removed and cells were washed with 1X PBS. Cells were then incubated  in media prepared with exosome depleted FBS in standard cell culture conditions for 48 hours.

tag: knockdown


title: C2G2Res2_R1

description:
27_5-Htt+-_PS_resilient_6
Gene-wise_read_countings.csv


title: Slide-338-06-02-2022-005-Non-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 609
DSP-1001660005138-B-G08

value: Stroma


title: WT_2h-2


title: IC_RBM24_1

description: 48 hours after media change, media was collected and spun down at 500g and passed through 0.4 um to remove any cells. 1 ml cell free media was taken for RNA isolation from CM. The rest of the media was used for exosome isolation by adding Polyethylene Glycol 10000 (PEG, HR2-607) to 10 % final and overnight incubation at 4C. The next day PEG/media mixture was spun down at 3000g at 4C for 1 hour. Supernatant was removed. We moved forward with isolating RNA fromthe pellets.


title: C1G2Res0_R7

description:
145_5-Htt+-_C_C_4
Gene-wise_read_countings.csv

value: no stress


title: Slide-342-06-02-2022-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 614
DSP-1001660005138-B-H02


title: Slide-338-06-02-2022-005-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 608
DSP-1001660005138-B-G07


title: C1G2Res0_R6

description:
140_5-Htt+-_C_C_4
Gene-wise_read_countings.csv


title: IC_HNRNPA2B1_2


title: WT_2h-1


title: C1G2Res0_R5

description:
136_5-Htt+-_C_C_4
Gene-wise_read_countings.csv


title: CCM02-2


title: IC_HNRNPA2B1_1


title: Slide-338-06-02-2022-004-Non-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 607
DSP-1001660005138-B-G06


title: WT_0h-3

value: log phase culture

value: YES medium


title: Slide-338-06-02-2022-004-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 606
DSP-1001660005138-B-G05


title: C1G2Res0_R4

description:
54_5-Htt+-_C_C_4
Gene-wise_read_countings.csv


title: C1G2Res0_R3

description:
52_5-Htt+-_C_C_4
Gene-wise_read_countings.csv


title: C1G2Res0_R2

description:
25_5-Htt+-_C_C_4
Gene-wise_read_countings.csv


title: IC_CtrlB_1

value: Control


title: WT_0h-1


title: Slide-332-06-01-2022-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 604
DSP-1001660005138-B-F04


title: C1G2Res0_R1

description:
22_5-Htt+-_C_C_4
Gene-wise_read_countings.csv


title: Slide-332-06-01-2022-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 603
DSP-1001660005138-B-F03


title: ecl123del_48h_biol_rep_3

description: h- ecl1∆::hygMX ecl2∆::natMX ecl3∆::kanMX

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
Resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts
Supplementary files format and content: DESeq2 output file

source_name: yeast

extract_protocol:
Hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA seq

tag: lab strain number

tag: growth conditions

value: 48h phosphate starved culture, ePMGT(-PO4) medium

value: yeast

value: ecl1, ecl2, ecl3 knockout


title: IC_CtrlA_1


title: Slide-332-06-01-2022-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 605
DSP-1001660005138-B-F05


title: EV_RBM24_2


title: Slide-332-06-01-2022-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 602
DSP-1001660005138-B-F02


title: Hindbrain vestibular neurons, phox2a-/-, replicate 2

value: 72-74 hours post-fertilization

value: Hindbrain vestibular neurons

value: Tg(-6.7Tru.Hcrtr2:GAL4-VP16); Tg(UAS:E1b-Kaede); Tg(isl1:GFP); phox2a-/-


title: patient_AML3_untreated

data_processing:
CLC Bio, V23
Normalization
Clustering
Cell identification and annotation with sc_human_cell_type_classifier_v1.2
Assembly: GRCh38
Supplementary files format and content: text file

extract_protocol:
10x Genomics Chromium Controller and the Chromium Single Cell 3′ Library & Gel Bead Kit (PN-120237) following the standard manufacturer’s protocol
Final library quality was assessed using an Agilent Tapestation

value: BM

value: untreated


title: ecl123del_48h_biol_rep_1


title: ecl123del_48h_biol_rep_2


title: Slide-332-06-01-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 601
DSP-1001660005138-B-F01


title: IC_CtrlB_2

description: 48 hours after media change, media was collected and spun down at 500g and passed through 0.4 um to remove any cells. 1 ml cell free media was taken for RNA isolation from CM. The rest of the media was used for exosome isolation by adding Polyethylene Glycol 10000 (PEG, HR2-607) to 10 % final and overnight incubation at 4C. The next day PEG/media mixture was spun down at 3000g at 4C for 1 hour. Supernatant was removed. We moved forward with isolating RNA fromthe pellets.

value: IC


title: ecl123del_36h_biol_rep_3

value: 36h phosphate starved culture, ePMGT(-PO4) medium


title: patient_AML3_treated

value: interferon gama 10 ng/ml


title: EV_RBM24_1

value: EV


title: WT_0h-2

value: h-


title: SLX

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

description: 10x Genomics

data_processing:
Raw sequencing reads of ST spots were quality checked and mapped to human GRch38 genome by STAR v2.7.3a (https://github.com/alexdobin/STAR).
Barcode and UMI counting were performed with Space Ranger v1.3.0 count module (https://support.10xgenomics.com/spatial-gene-expression/software) to generate feature-barcode matrix. Spots with fewer than 200 detected gene counts were discarded.
For dimension reduction and clustering, we computed the top principal components (PCs) based on the expression profiles of the top 2000 most variable genes by the FindVariableFeatures function in R package Seurat v4.3.0.
Dimension reduction was performed using principal component analysis (PCA) and the first ten PCs were used to generate clusters by K-means algorithm and graph-based algorithm, respectively. The resolution of clustering was 0.8. The spots were visualized by the uniform manifold approximation and projection (UMAP) algorithm.
For spot annotation (i.e., assignment of dominant cell types or tissue architecture to each cluster), we scored each cluster by curated cell-type specific marker genes and signatures, and by knowledge-based assignment according to anatomic morphology and structure revealed by H&E staining.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: Prostate cancer

extract_protocol:
Fresh samples were preserved in OCT and processed by standard Cryo-sectioning technique, followed by a quick H&E staining of one slide to view tissue histology.
According to the manufacture’s introduction, ST libraries were constructed using Visum spatial library construction kit (10x Genomics, PN-1000184). For each well, slide cassette was used to create leakproof wells for adding reagents. Then, 70μl permeabilization enzyme were added and incubated at 37°C for 18 min. Each well was washed with 100μl SSC, and 75μl reverse transcription master mix was added for cDNA synthesis. cDNA amplification was performed on a S1000TM Touch Thermal Cycler (Bio Rad). The libraries were finally sequenced using an Illumina Nova-seq 6000 platform.

value: Prostate cancer


title: IC_CtrlA_2


title: Slide-327-05-18-2022-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 599
DSP-1001660005138-B-E07

value: Stroma


title: Slide-332-06-01-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 600
DSP-1001660005138-B-E12

value: Tumor


title: ecl123del_36h_biol_rep_2


title: EV_HNRNPA2B1_2


title: EV_CtrlB_2

value: Control


title: RJZ

description: 10x Genomics


title: ecl123del_24h_biol_rep_2

value: 24h phosphate starved culture, ePMGT(-PO4) medium


title: Slide-327-05-18-2022-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 597
DSP-1001660005138-B-E05


title: EV_CtrlB_1


title: Slide-327-05-18-2022-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 596
DSP-1001660005138-B-E04


title: ecl123del_24h_biol_rep_3

value: yeast


title: PRS

description: 10x Genomics


title: LGL

description: 10x Genomics


title: Slide-327-05-18-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 595
DSP-1001660005138-B-E03


title: JLR

description: 10x Genomics


title: EV_CtrlA_2


title: ecl123del_24h_biol_rep_1

value: ecl1, ecl2, ecl3 knockout


title: EV_CtrlA_1


title: ecl123del_12h_biol_rep_3

value: 12h phosphate starved culture, ePMGT(-PO4) medium


title: HB

description: 10x Genomics


title: CFX

description: 10x Genomics


title: ecl123del_12h_biol_rep_2


title: EV_HNRNPA2B1_1


title: Slide-333-05-18-2022-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 593
DSP-1001660005138-B-E01


title: Slide-327-05-18-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 594
DSP-1001660005138-B-E02


title: ecl123del_36h_biol_rep_1


title: CDZ

description: 10x Genomics


title: RJZ-SCLPC

description: 10x Genomics

data_processing:
Standard pipelines of Cell Ranger (https://support.10xgenomics.com/spatial-gene-expression/software) were used to perform data processing and alignment to human GRch38 genome with default parameters.
Filtering, barcode counting, and UMI counting were performed with Cell Ranger count module to generate feature-barcode matrix and determine clusters.
Cells whose gene number was less than 200, or gene number ranked in the top 1%, or mitochondrial gene ratio was more than 25% were considered as abnormal and thus filtered out.
Dimension reduction was performed using PCA and visualization was realized by UMAP.
Cluster annotation was performed by curated cell-type specific marker genes and signatures.
Assembly: hg38
Supplementary files format and content: Tab-seperated values files
Supplementary files format and content: Matrix files

molecule: nuclear RNA

extract_protocol:
Two cryopreserved PCa tissues were enzymatically digested and single nucleus were counted and collected.
Briefly, using single cell 3 'Library and Gel Bead Kit V3.1(10x Genomics, 1000121) and Chromium Single Cell G Chip Kit (10x Genomics, 1000120), the cell suspension (300-600 cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cell will be recovered was estimated to be about 3,000 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing). Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 according to the manufacture’s introduction, and finally sequenced by Illumina Nova-seq 6000 platform.
snRNA-seq


title: IVCL scRNA-seq

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

description: 10x Genomics

data_processing:
scRNAseq fastq files were processed via CellRanger 3.0.2 and mapped to mm10 genome.
Assembly: mm10
Supplementary files format and content: Cellranger filtered features, barcodes and matrix files

source_name: Mixed liver single cell suspension

growth_protocol: Starting at 8-10 weeks of age, C57B6 mice were underwent partial inferior vena cava ligation to induce portal hypertension for 6 weeks before sacrifice.

extract_protocol:
Mice non-parenchymal cells were isolated using previously published protocols. Primary mice hepatocytes were isolated using a modification of the two-step collagenase perfusion method. Cell viability was >95% as measured by Trypan Blue staining.
For scRNAseq:Samples were then prepared as outlined by the 10x Genomics Single Cell 3v2 Reagent Kit user guide. Briefly, the samples were washed twice in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. Following counting, the appropriate volume for each sample was calculated for a target capture of 12000 cells. Samples were loaded onto the 10x Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen): cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).
The molarity of each library was calculated based on library size as measured using a bioanalyzer (Agilent Technologies) and qPCR amplification data (Kappa/Roche). Samples were pooled and normalized to 10 nM, then diluted to 2 nM using elution buffer (Qiagen) with 0.1% Tween20 (Sigma). Each 2 nM pool was denatured using 0.1 N NaOH at equal volumes for 5 min at room temperature. Library pools were further diluted to 20 pM using HT-1 (Illumina) before being diluted to a final loading concentration of 14 pM. 150 μl from the 14 pM pool was loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1—26 cycles, read 2—98 cycles, index 1—8 cycles.

value: Liver

value: pIVCL


title: C2G2Res2_R6

description:
Counts_ChIP-Seq_HttxPS.csv
89

data_processing:
mapping using Bowtie2 (v2.1.0) software in end-to-end & sensitive-mode
coverage peaks were generated using MACS 14 peak caller (Zhang et al. 2008). Subsequently, peaks were aligned and sequencing reads within overlapping peak sets were counted using the DiffBind R-package v2.0.9 (Stark & Brown 2013).
statistics were performed using the DeSeq2 R package (Love et al. 2014)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Read overlapping with called peaks

extract_protocol:
brains were extracted, snapfrozen in isopentane, subsequently the hippocampus was dissected,hippocampi of both hemispheres were powderised at - 80 ͦC, blended and split in two equal portions. the portion used for the epigenetic investigation was further split in two equal portions of which one was used for the ChIP experiments. For chromatin immunoprecipitation, targeting H3K4me3, DNA was fixated, sonicated, followed by antibody based capture and several washings. Following decrosslinking,  DNA was extracted from one portion, using regular phenol/chlorophorm based extraction protocol as published in (Schraut et al. 2014)
library preparation was performed by Nxt-Dx (Ghent, Belgium), using the NEBNext Ultra II DNA Library prep kit for Illumina (NEB, Ipswitch, Massachusetts, USA).

treatment_protocol: dams were exposed to restraint stress three times per day from embryonic day 13 to embryonic day 17; adult female offspring were investigated

value: hippocampus

value: 3 months

value: PS-resilient

tag: chip antibody

value: H3K4me3:39159, Active motif, Carlsbad, CA, USA


title: Slide-327-05-18-2022-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 598
DSP-1001660005138-B-E06

data_processing:
*library strategy: GeoMx DSP (RNA-seq)
Illumina FASTQ sequencing files were processed using the GeoMx NGS Pipeline version 2.3.3.10 to generate digital count conversion (DCC) files which were subsequently analyzed using the GeoMx DSP Analysis Suite version 2.4.1 to perform data QC and Q3 normalization using all target groups
Assembly: GeoMx Cancer Transcriptome Atlas
Supplementary files format and content: Processed data files are provided in DCC format

extract_protocol:
Spatial profiling was performed on three regions of interests (ROIs) from formalin fixed paraffin embedded tissue (FFPE) sections for each patient sample. Tumor epithelial compartment (highlighted by pan-cytokeratin, green-fluorescent marker) and the stroma compartment (pan-cytokeratin negative).
This involved library preparation and assessing the quality and quantity of the purified library using Agilent Bioanalyzer and Qubit assays, respectively. NGS libraries were sequenced using the Illumina NextSeq 550 instrument


title: ecl123del_12h_biol_rep_1


title: Healthy scRNA-seq

description: 10x Genomics


title: Slide-333-05-18-2022-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 592
DSP-1001660005138-B-D12


title: ecl123del_8h_biol_rep_3

value: 8h phosphate starved culture, ePMGT(-PO4) medium


title: Slide-328-05-18-2022-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 589
DSP-1001660005138-B-D07


title: C2G2Res2_R3

description:
Counts_ChIP-Seq_HttxPS.csv
63


title: ecl123del_4h_biol_rep_3

value: 4h phosphate starved culture, ePMGT(-PO4) medium


title: C2G2Res2_R5

description:
Counts_ChIP-Seq_HttxPS.csv
27


title: Slide-333-05-18-2022-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 591
DSP-1001660005138-B-D11


title: HB-Adeno

description: 10x Genomics


title: Patient5,Peak,neg_TCR

city: Barcelona

first: Mercedes

last: Guerrero Murillo

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles, s/n,

country: Spain

institute: Institut de Recerca contra la Leucèmia Josep Carreras

library_source: other

data_processing:
Cell Ranger (v3.1.0, 10x Genomics) was used to align reads to the human reference genome (hg38).
Assembly: hg38
Supplementary files format and content: Matrix, barcode and feature files were generated using Cell Ranger count (10x Genomics).
Library strategy: scTCR-seq

molecule: other

source_name: T cell

extract_protocol:
CARpos and CARneg CD3+ T-cells were FACS-sorted at high purity (>95%) using a FACS Aria flow cytometer (BD Biosciences, San Jose, CA)
Chromium Single Cell 5´ Library and Gel Bead Kit v1.0 (10× Genomics, #1000006) & the Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (10× Genomics, #1000005)

value: T cell


title: Slide-333-05-18-2022-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 590
DSP-1001660005138-B-D10


title: C2G2Res2_R2

description:
Counts_ChIP-Seq_HttxPS.csv
106


title: C2G2Res2_R4

description:
Counts_ChIP-Seq_HttxPS.csv
90


title: ecl123del_8h_biol_rep_1

description: h- ecl1∆::hygMX ecl2∆::natMX ecl3∆::kanMX


title: Patient5,Peak,pos

data_processing:
Cell Ranger (v3.1.0, 10x Genomics) was used to align reads to the human reference genome (hg38).
Assembly: hg38
Supplementary files format and content: Matrix, barcode and feature files were generated using Cell Ranger count (10x Genomics).


title: Patient5,Peak,neg


title: Slide-328-05-18-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 587
DSP-1001660005138-B-D03


title: Slide-328-05-18-2022-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 588
DSP-1001660005138-B-D06


title: ecl123del_4h_biol_rep_2


title: Slide-328-05-18-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 586
DSP-1001660005138-B-D02


title: ecl123del_8h_biol_rep_2


title: C2G2Res2_control

description:
input control not treated
none
127IN


title: C2G2Res2_R1

description:
Counts_ChIP-Seq_HttxPS.csv
127


title: Patient5,IP,pos


title: slide Final-345-05-13-22-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 585
DSP-1001660005138-B-D01


title: ecl123del_4h_biol_rep_1


title: ecl123del_0h_biol_rep_2

value: log phase culture, YES medium


title: ecl123del_0h_biol_rep_3


title: Patient5,IP,pos_TCR


title: C2G2Res1_R6

description:
Counts_ChIP-Seq_HttxPS.csv
37

value: PS-susceptible


title: slide Final-345-05-13-22-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 584
DSP-1001660005138-B-C12

value: Tumor


title: C2G2Res1_R5

description:
Counts_ChIP-Seq_HttxPS.csv
58


title: Patient5,Peak,pos_TCR


title: ecl123del_0h_biol_rep_1


title: C2G2Res1_R4

description:
Counts_ChIP-Seq_HttxPS.csv
76


title: Patient5,IP,neg


title: h- ecl1∆::hygMX ecl2∆::natMX ecl3∆::kanMX, rep3

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
Resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts

source_name: Schizosaccharomyces pombe

growth_protocol: Log phase cultures grown at 30˚C in YES medium

value: Schizosaccharomyces pombe

tag: developmental stage

value: Vegetative growth


title: slide Final-345-05-13-22-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 583
DSP-1001660005138-B-C11

value: Stroma


title: slide Final-345-05-13-22-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 582
DSP-1001660005138-B-C10


title: h- ecl1∆::hygMX ecl2∆::natMX ecl3∆::kanMX, rep1

value: ecl1, ecl2, ecl3 knockout


title: slide Final-345-05-13-22-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 580
DSP-1001660005138-B-C08


title: slide Final-345-05-13-22-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 581
DSP-1001660005138-B-C09


title: Patient4,Peak,neg


title: Patient4,Peak,pos


title: h- ecl1∆::hygMX ecl2∆::natMX ecl3∆::kanMX, rep2


title: Patient4,Peak,pos_TCR


title: h- ecl3∆::kanMX, rep2

value: ecl3 knockout


title: C2G2Res1_R2

description:
Counts_ChIP-Seq_HttxPS.csv
122


title: C2G2Res1_R3

description:
Counts_ChIP-Seq_HttxPS.csv
121


title: slide-315-05-13-22-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 578
DSP-1001660005138-B-C06


title: C2G2Res1_R1

description:
Counts_ChIP-Seq_HttxPS.csv
103


title: C2G2Res1_control

description:
input control not treated
none
122IN


title: Patient4,IP,pos_TCR


title: Patient4,Peak,neg_TCR


title: Patient4,IP,pos


title: slide-315-05-13-22-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 577
DSP-1001660005138-B-C05


title: C2G1Res2_R6

description:
Counts_ChIP-Seq_HttxPS.csv
57


title: Patient5,IP,neg_TCR


title: h- ecl3∆::kanMX, rep1


title: slide-315-05-13-22-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 576
DSP-1001660005138-B-C04


title: C2G1Res2_R4

description:
Counts_ChIP-Seq_HttxPS.csv
45


title: C2G1Res2_R5

description:
Counts_ChIP-Seq_HttxPS.csv
117


title: slide-315-05-13-22-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 575
DSP-1001660005138-B-C03


title: h- , rep3

value: WT


title: h- , rep2


title: Patient4,IP,neg_TCR


title: Patient4,IP,neg


title: slide-315-05-13-22-004-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 579
DSP-1001660005138-B-C07


title: h- ecl3∆::kanMX, rep3


title: h- , rep1


title: C2G1Res2_R3

description:
Counts_ChIP-Seq_HttxPS.csv
42


title: Patient3,Peak,pos_TCR


title: slide-315-05-13-22-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 574
DSP-1001660005138-B-C02


title: C2G1Res2_R1

description:
Counts_ChIP-Seq_HttxPS.csv
110


title: C2G1Res2_R2

description:
Counts_ChIP-Seq_HttxPS.csv
75


title: slide-314-05-13-22-005-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 572
DSP-1001660005138-B-B12


title: Patient3,Peak,neg_TCR


title: C2G1Res2_control

description:
input control not treated
none
57IN


title: C2G1Res1_R6

description:
Counts_ChIP-Seq_HttxPS.csv
66


title: slide-314-05-13-22-004-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 571
DSP-1001660005138-B-B11


title: pho7_48h-2

first: Angad

last: Garg

state: New York

value: 48 h phopshate starved culture, ePMGT(-PO4) medium

value: ePMGT(-PO4) medium

value: h- pho7delta::natMX


title: Patient3,Peak,neg


title: pho7_36h-3

value: 36 h phopshate starved culture, ePMGT(-PO4) medium


title: pho7_48h-1


title: Patient3,IP,pos_TCR


title: slide-314-05-13-22-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 569
DSP-1001660005138-B-B09


title: slide-314-05-13-22-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 570
DSP-1001660005138-B-B10


title: C2G1Res1_R5

description:
Counts_ChIP-Seq_HttxPS.csv
60

value: hippocampus

value: 3 months

value: H3K4me3:39159, Active motif, Carlsbad, CA, USA


title: Patient3,IP,pos

value: T cell


title: pho7_36h-2


title: slide-314-05-13-22-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 568
DSP-1001660005138-B-B08


title: C2G1Res1_R3

description:
Counts_ChIP-Seq_HttxPS.csv
48


title: C2G1Res1_R4

description:
Counts_ChIP-Seq_HttxPS.csv
34


title: pho7_48h-3


title: slide-314-05-13-22-006-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 573
DSP-1001660005138-B-C01


title: pho7_24h-3

value: 24 h phopshate starved culture, ePMGT(-PO4) medium


title: Slide-311-05-11-2022-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 567
DSP-1001660005138-B-B07


title: Patient3,Peak,pos


title: Patient3,IP,neg


title: C2G1Res1_R2

description:
Counts_ChIP-Seq_HttxPS.csv
50

value: PS-susceptible


title: pho7_24h-2


title: pho7_24h-1


title: C2G1Res1_R1

description:
Counts_ChIP-Seq_HttxPS.csv
84


title: Patient2,Peak,pos_TCR


title: C1G2Res0_R6

description:
Counts_ChIP-Seq_HttxPS.csv
25

value: no stress


title: pho7_36h-1


title: pho7_12h-2

value: 12 h phopshate starved culture, ePMGT(-PO4) medium


title: Patient2,Peak,pos


title: Slide-311-05-11-2022-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 565
DSP-1001660005138-B-B05


title: C2G1Res1_control

description:
input control not treated
none
60IN


title: pho7_12h-3


title: Slide-311-05-11-2022-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 564
DSP-1001660005138-B-B04

value: Tumor


title: Slide-341-05-11-2022-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 561
DSP-1001660005138-B-B01

value: Stroma


title: Patient2,Peak,neg_TCR


title: Slide-341-05-11-2022-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 560
DSP-1001660005138-B-A12


title: Slide-341-05-11-2022-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 559
DSP-1001660005138-B-A11


title: Patient2,Peak,neg


title: C1G2Res0_R2

description:
Counts_ChIP-Seq_HttxPS.csv
139


title: pho7_8h-2

value: 8 h phopshate starved culture, ePMGT(-PO4) medium


title: Patient2,IP,neg


title: C1G2Res0_R5

description:
Counts_ChIP-Seq_HttxPS.csv
22


title: Patient3,IP,neg_TCR


title: pho7_12h-1


title: Patient2,IP,pos_TCR


title: Slide-341-05-11-2022-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 558
DSP-1001660005138-B-A10


title: Patient1,Peak,pos_TCR


title: C1G2Res0_R4

description:
Counts_ChIP-Seq_HttxPS.csv
17


title: Slide-311-05-11-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 562
DSP-1001660005138-B-B02


title: pho7_8h-3


title: Patient2,IP,pos


title: C1G2Res0_control

description:
input control not treated
none
54IN


title: C1G2Res0_R3

description:
Counts_ChIP-Seq_HttxPS.csv
52


title: C1G1Res0_R6

description:
Counts_ChIP-Seq_HttxPS.csv
79


title: pho7_8h-1


title: Slide-311-05-11-2022-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 566
DSP-1001660005138-B-B06


title: Patient2,IP,neg_TCR


title: Slide-311-05-11-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 563
DSP-1001660005138-B-B03


title: pho7_4h-3

value: 4 h phopshate starved culture, ePMGT(-PO4) medium


title: pho7_0h-3

value: log phase culture

value: YES medium


title: Patient1,Peak,neg


title: Slide-353-05-11-2022-003-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 555
DSP-1001660005138-B-A07


title: Slide-353-05-11-2022-003-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 554
DSP-1001660005138-B-A06


title: Slide-341-05-11-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 556
DSP-1001660005138-B-A08


title: Patient1,Peak,pos


title: pho7_4h-2

value: ePMGT(-PO4) medium


title: Slide-341-05-11-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 557
DSP-1001660005138-B-A09


title: Patient1,IP,pos_TCR


title: pho7_0h-1

value: h- pho7delta::natMX


title: pho7_4h-1


title: C1G1Res0_R4

description:
Counts_ChIP-Seq_HttxPS.csv
26


title: Slide-353-05-11-2022-002-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 552
DSP-1001660005138-B-A04


title: Patient1,Peak,neg_TCR


title: Patient1,IP,pos


title: C1G1Res0_R5

description:
Counts_ChIP-Seq_HttxPS.csv
23


title: WT_0h-3

value: h-


title: C1G1Res0_R1

description:
Counts_ChIP-Seq_HttxPS.csv
78

value: hippocampus


title: pho7_0h-2


title: WT_0h-2


title: C1G1Res0_R3

description:
Counts_ChIP-Seq_HttxPS.csv
53

value: 3 months


title: Slide-353-05-11-2022-002-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 553
DSP-1001660005138-B-A05


title: C1G1Res0_control

description:
input control not treated
none
53IN


title: Patient1,IP,neg_TCR


title: Slide-353-05-11-2022-001-Epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 550
DSP-1001660005138-B-A02


title: WT_0h-1


title: Patient1,IP,neg


title: C1G2Res0_R1

description:
Counts_ChIP-Seq_HttxPS.csv
54

value: H3K4me3:39159, Active motif, Carlsbad, CA, USA


title: SP-EPN 258

status: Public on Jan 26 2024

type: genomic

city: Hamburg

first: Karoline

last: Hack

address: Martinistraße 52

department: Children's Cancer Center Hamburg

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Methylation data were processed using minfi and noob normalization. CpG sites associated with SNPs and sex chromosomes were excluded.

label: Cy3 and Cy5

source_name: Spinal ependymoma

label_protocol: not provided

extract_protocol: DNA was extracted from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega). About 100-500 ng DNA were used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

value: Spinal ependymoma (FFPE tissue)

tag: array type

value: EPIC

tag: material type

value: FFPE


title: C1G1Res0_R2

description:
Counts_ChIP-Seq_HttxPS.csv
128

value: no stress

tag: genotype


title: SP-EPN 255

tag: tissue


title: SP-EPN 257


title: SP-EPN 256


title: SP-EPN 251


title: SP-EPN 253


title: SP-EPN 250


title: SP-EPN 252


title: SP-EPN 249

value: Cryo


title: SP-EPN 246


title: SP-EPN 248


title: SP-EPN 247


title: SP-EPN 237


title: SP-EPN 239


title: SP-EPN 241


title: SP-EPN 234


title: SP-EPN 236


title: Slide-353-05-11-2022-001-Non-epi

description:
GeoMx Digital Spatial Profiling (DSP) platform & Illumina NextSeq 551
DSP-1001660005138-B-A03


title: SP-EPN 242


title: SP-EPN 245


title: SP-EPN 243


title: SP-EPN 244


title: SP-EPN 240


title: SP-EPN 233


title: SP-EPN 225


title: SP-EPN 227


title: SP-EPN 230


title: SP-EPN 229


title: quadriceps muscle, D1mck484het

city: Los Angeles

first: Peter

middle: Huy

last: Tran

address: 650 Charles E Young Dr. S

department: Medicine

institute: UCLA

data_processing:
Raw reads were checked for quality using FastQC, aligned to the Mus musculus GRCm38, and then counted using Mus musculus GRCm38 version 97. Alignment and counting occurred used Rsubread v 2.4.2. Raw counts were then analyzed for differential gene expression using the DESeq2 v1.30.0
Assembly: Grcm38
Supplementary files format and content: Excel file represents CPMs

source_name: quadriceps muscle

extract_protocol:
Frozen muscle samples were homogenized using a tissue homogenizer in Trizol. RNA was isolated using the Qiagen RNeasy Mini QIAcube Kit following the manufacturer’s instructions. The concentration and purity of isolated RNA were determined using a NanoDrop (Invitrogen) and the Agilent TapeStation separately. Only samples with RIN > 7.0 were used.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit and RiboZero Gold following the manufacturer’s instructions.
The resulting libraries were combined into two pools and sequenced on an Illumina Sequencing by Synthesis (SBS) HiSeq 4000 analyzer within the UCLA Neuroscience Genomics Core facility.

value: quadriceps muscle

tag: mouse model

tag: treatment

value: normal chow diet


title: quadriceps muscle, D1mck473het


title: quadriceps muscle, D1mck486c

value: Control f/f

value: Control


title: SP-EPN 232


title: Lung, Sample 3

city: Houston

first: Pawel

middle: Karol

last: Mazur

state: TX

address: 1515 Holcombe Blvd.

institute: University of Texas MD Anderson Cancer Center

data_processing:
Quality controls of fastq files (fastqc software).
Merge paired-end reads (PANDA-seq software)
Reads filtering and trimming for barcode clustering (DADA2 software)
Training of error model on known sequences (DADA2 software)
Downstream analysis (GC correction, tumor size, tumor number and other quantifications - tuba-seq package )
Assembly: mm39
Supplementary files format and content: Cell numbers accumulated across all six samples used in tuba sequencing.
Library strategy: Tuba-seq (Tumor barcoding sequencing)

source_name: Lung

extract_protocol:
2% Agarose gel electrophoresis followed by DNA purification
one-step PCR

value: Lung

tag: cell line

tag: cell type

value: Small cell lung cancer


title: quadriceps muscle, D1mck469het


title: SP-EPN 228


title: SP-EPN 224


title: quadriceps muscle, D1mck485c


title: Lung, Sample 2


title: SP-EPN 223


title: SP-EPN 222


title: SP-EPN 218


title: SP-EPN 221


title: SP-EPN 219


title: Lung, Sample 1


title: SP-EPN 217


title: thymus_CD8,replicate3

city: Wuhan

first: Pingping

last: Han

state: Hubei

address: Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

description: thymus_CD8 is named CD8_t in the manuscript

data_processing:
Quality control of raw FASTQ data to remove adapter sequences,reads with ploy-N, low-quality reads, and clean reads were obtained for subsequent analysis using an in-house Perl script, performed by Beijing Novogene Bioinformatics Technology Company
The porcine reference genome (Sscrofa 11.1) and gene annotation files (v11.1.98) were downloaded from the Ensemble website
We utilized STAR (v2.7.5a) to build reference genome index files and align paired-end clean reads to the reference genome.
Gene quantification was performed using RSEM (v 1.2.31). The raw counts, FPKM (fragments per kilobase of transcripts per million mapped fragments) value and TPM (transcripts per million) values of each gene or isoform were contained in the output files.
Assembly: Sscrofa 11.1
Supplementary files format and content: tab-delimited text file include raw counts for each sample

organism: Sus scrofa domesticus

source_name: thymus

extract_protocol:
Total RNA was extracted from each T cell population using a RNeasy Mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol with three biological replicates. RNA purity and concentration were determined using a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA).
The cDNA library construction and sequencing were carried out in accordance with the Illumina standard protocol by Beijing Novogene Bioinformatics Technology Company. The library quality was evaluated using an Agilent Bioanalyzer 2100 system. The cDNA library was sequenced on an Illumina Hiseq platform, and 150bp paired-end reads were generated.

treatment_protocol: Fresh thymic and mesenteric lymph node tissues were obtained from 3 pigs and were washed with cold phosphate-buffered saline (PBS). Subsequently, the thymic and mesenteric lymph node tissues were minced and digested with 1mg/mL and 2 mg/mL collagenase I for 1 h at 37℃, respectively. Equal volumes of 5% fetal bovine serum were added to terminate the digestion reaction. The dissociated cells were filtered through a 100 µm cell strainer, centrifuged at 1000 rpm for 10 min at 4°C, and diluted to 1×106/mL. The quantity and viability of diluted cells were assessed using trypan blue staining.Seven T cell subpopulations were sorted by flow cytometry

value: thymus


title: young lumbar disc

city: Stanford

first: Malachia

last: Hoover

address: 265 Campus Drive Room G3105

institute: Stanford University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 5.0.0.
Assembly: mm10
Supplementary files format and content: csv file containing a raw counts matrix.

source_name: Lumbar disc 3

growth_protocol: lumbar intervertebral disc 3 was dissected from a 8-week-old mouse

extract_protocol:
Lumbar intervertebral disc 3 was carefully dissected from a 8-week-old mouse and then subjected to mechanical seperation and then collagenase digestion while incubating at 37 degrees Celcius for 1 hours . Following this, the solution underwent centrifugation, post which the supernatant was carefully discarded. The residual cell pellet was then resuspended in FACS buffer solution and live cells were isolated via Trypan blue staining.
Library was performed according to the manufacturer's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, intervertebral disc cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains the R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, pair-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: the designated region-of-interest (ROI) was carefully dissected

value: Lumbar disc 3

value: intervertebral disc cells

tag: age

value: 8 weeks old


title: quadriceps muscle, D1mck487c


title: thymus_CD8,replicate2


title: Lung, Sample 5


title: SP-EPN 215


title: thymus_CD8,replicate1


title: Lung, Sample 6


title: Lung, Sample 4


title: thymus_CD4,replicate2

description: thymus_CD4 is named CD4_t in the manuscript


title: SP-EPN 214


title: thymus_CD4,replicate3


title: SP-EPN 210


title: SP-EPN 216


title: SP-EPN 207


title: SP-EPN 208


title: SP-EPN 203


title: SP-EPN 201


title: SP-EPN 200


title: thymus_NP,replicate2

description: thymus_NP is named CD4-CD8-_t in the manuscript


title: lymph_CD8,replicate2

description: lymph_CD8 is named CD8_l in the manuscript

source_name: mesenteric lymph node

value: mesenteric lymph node


title: thymus_NP,replicate3


title: thymus_DP,replicate3

description: thymus_DP is named CD4+CD8+_t in the manuscript


title: thymus_NP,replicate1


title: thymus_CD4,replicate1


title: lymph_CD8,replicate1


title: SP-EPN 199


title: lymph_CD8,replicate3


title: thymus_DP,replicate2


title: SP-EPN 213


title: SP-EPN 198


title: lymph_CD4,replicate2

description: lymph_CD4 is named CD4_l in the manuscript


title: thymus_DP,replicate1


title: lymph_DN,replicate3

description: lymph_DN is named CD4-CD8-_l in the manuscript


title: SP-EPN 209


title: lymph_DN,replicate2


title: SP-EPN 195


title: SP-EPN 193


title: SP-EPN 211


title: lymph_DN,replicate1


title: SP-EPN 190


title: Dicer WT, mock, rep1

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
RNA-seq data were processed and analyzed using the following workflow.
The first 5'-end base of each read, a T-overhang added during the library preparation with the Illumina Stranded mRNA protocol, was first trimmed, before using Skewer v0.2.2 in paired-end mode for average quality read filtering and adapter trimming (command: skewer -Q 25 -x CTGTCTCTTATACACATCT -y CTGTCTCTTATACACATCT -l 31 -m pe -t 2 -o <name> --quiet <name>_R1.fq <name>_R2.fq).
Sample quality checks were performed before and after these preprocessing steps using FastQC v0.11.8.
Then, human full-length protein-coding transcripts (GENCODE Human (GRCh38.p13) release 41) and SINV-GFP both genomic and subgenomic transcripts (private sequences derived from NC_001547.1) were quantified using Salmon v1.10.0 in mapping-based mode with the selective alignment algorithm and a decoy-aware transcriptome (command: salmon quant -p 6 -i index/gencode41.hg38.sinv.decoys_index --libType A --seqBias --gcBias --numBootstraps 30 -1 data/<name>_preprocessed_R1.fq.gz -2 data/<name>_preprocessed_R2.fq.gz -o salmon-quants/<name>).
Transcript-level abundance and count estimates thus obtained were next imported into R and further analyzed with the tximport and DESeq2 packages. Briefly, original transcript-level counts were summarized to gene-level estimated counts and an offset was produced from transcript-level abundance estimates to correct for changes to the average transcript length across samples. Differential expression analyses between tested conditions were then conducted at the gene-level, and statistical significance was defined with an adjusted p-value < 0.05 and an absolute log2 fold change > 1 thresholds.
Finally, gene set enrichment analysis (GSEA) studies were performed using the GSEA_4.3.2 Mac application, as made available by the Broad Institute and the University of California, San Diego (https://www.gsea-msigdb.org/gsea/index.jsp). These analyses were conducted on the DESeq2 normalized counts of each comparison dataset against the Hallmark Gene Sets (v2023.1) provided by the Molecular Signatures Database (MSigDB), and by using the Human_Ensembl_Gene_ID_MSigDB.v2023.1.Hs.chip  annotation file and all other parameters by default, except the permutation type which was set to gene_set
Assembly: GRCh38.p13 + private sequence derived from NC_001547.1
Supplementary files format and content: salmon_quants.txt: tab-delimited text file with Salmon quantification of studied transcripts in each sample
Supplementary files format and content: deseq2_normcounts.txt: tab-delimited text file with DESeq2 normalized gene counts in each sample

growth_protocol: NoDice FHA:DICER WT #4 or N1 #6 cells were plated in P100mm petri dishes at 5 000 000 cells per dish and infected the following day with SINV-GFP at an MOI of 2 for 12 h or 0.02 for 24 h. Cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10 % fetal bovine serum in a humidified atmosphere with 5 % CO2 at 37°C.

extract_protocol:
Cells were collected in Trizol reagent (Invitrogen, Thermo Fisher Scientific) and RNAs were isolated according to the manufacturer’s instructions.
ssRNA-seq (stranded RNA-seq): RNA-Seq libraries were generated according to the manufacturer’s instructions from 250 ng of total RNA using the Illumina Stranded mRNA Prep, Ligation kit (Reference Guide - PN 1000000124518) and IDT for Illumina RNA UD Indexes Ligation (Illumina, San Diego, USA). Briefly, Oligo(dT) magnetic beads were used to purify and capture the mRNA molecules containing polyA tails.The purified mRNA were then fragmented at 94°C for 2 min and copied into first strand complementary DNA (cDNA) using reverse transcriptase and random primers. Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dUTP in place of dTTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Cells were infected with a modified version of Sindbis virus expressing GFP (SINV-GFP) at an MOI of 2 for 12 h or 0.02 for 24 h. Cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10 % fetal bovine serum in a humidified atmosphere with 5 % CO2 at 37°C.

value: Human embryonic kidney

value: NoDice FHA:DICER WT #4

tag: viral infection_conditions


title: Tumor 43

city: Manchester

first: Qing-Jun

last: Meng

state: Manchester

address: A.V.Hill Building, The University of Manchester, Oxford Road

department: Division of Cell Matrix Biology & Regenerative Medicine

country: United Kingdom

institute: University of Manchester

data_processing:
Raw reads of sequenced breast tumor and matched non-tumor adjacent samples were aligned to human genome (GRCh38) using STAR (version 2.5). The expression quantification step was performed with RSEM (version 1.3.0). The raw RSEM counts were transformed to TPM values. In the process of calculating TPM values, the gene length information was from the human gtf file (GRCh38) parsed by the refGenome package (version 1.7.7). For a gene with multiple transcript splice-isoforms, we selected the longest transcript as the representative gene length.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene_id, gene_name, trancriptLength

source_name: Human tumor breast tissue

extract_protocol:
RNA was isolated by Rneasy Lipid tissues mini kit (QIAGEN). 0.5-1.0 ug of total RNA was used for the construction of sequencing libraries. Quality and integrity of the RNA samples were assessed using a 2200 TapeStation (Agilent Technologies).
Libraries were generated by the Genomic Technologies Core Facility using the TruSeq® Stranded mRNA assay (Illumina, Inc.)

value: Human tumor breast tissue

tag: Sex

value: female

tag: subtype

value: Luminal A


title: Dicer N1, mock, rep3

value: NoDice FHA:DICER N1 #6


title: Dicer N1, mock, rep2


title: Normal 43

source_name: Human normal breast tissue

value: Human normal breast tissue

value: Normal


title: Dicer WT, mock, rep3


title: SP-EPN 197

value: Spinal ependymoma (FFPE tissue)

value: EPIC

value: Cryo


title: Normal 42


title: Dicer WT, mock, rep2


title: Tumor 42


title: Tumor 41


title: SP-EPN 191


title: Normal 41


title: Dicer N1, mock, rep1


title: SP-EPN 182

value: FFPE


title: SP-EPN 184


title: SP-EPN 186


title: SP-EPN 179


title: SP-EPN 187


title: SP-EPN 181


title: SP-EPN 183


title: SP-EPN 180


title: SP-EPN 178


title: Tumor 40


title: Normal 40


title: SP-EPN 176


title: SP-EPN 177


title: Tumor 39


title: SP-EPN 175


title: Normal 39


title: Normal 38


title: Tumor 38


title: SP-EPN 212


title: SP-EPN 169


title: Tumor 37


title: SP-EPN 158


title: SP-EPN 171


title: Normal 37


title: SP-EPN 166


title: SP-EPN 167


title: Normal 36


title: SP-EPN 161


title: Tumor 35


title: SP-EPN 168


title: Tumor 36


title: SP-EPN 159


title: SP-EPN 204


title: SP-EPN 157


title: Tumor 34


title: Normal 34


title: Normal 35


title: SP-EPN 160


title: SP-EPN 153


title: Tumor 33


title: Normal 33


title: Tumor 32


title: SP-EPN 20


title: SP-EPN 220


title: SP-EPN 17


title: Normal 32


title: Tumor 31


title: SP-EPN 9


title: SP-EPN 165


title: Normal 31


title: SP-EPN 155


title: Tumor 30

value: TNBC


title: lymph_CD4,replicate1


title: Normal 29


title: SP-EPN 149


title: SP-EPN 154


title: SP-EPN 150


title: SP-EPN 151


title: SP-EPN 152


title: Tumor 27


title: Normal 30


title: SP-EPN 147


title: Normal 27


title: Tumor 28


title: SP-EPN 148


title: lymph_CD4,replicate3


title: Tumor 26


title: Normal 26


title: Tumor 25

value: Luminal B


title: Normal 25


title: SP-EPN 164


title: Tumor 24


title: SP-EPN 77


title: Tumor 29


title: SP-EPN 79


title: Normal 24


title: Normal 28


title: SP-EPN 74


title: SP-EPN 76


title: Tumor 23


title: SP-EPN 73


title: SP-EPN 71


title: SP-EPN 72


title: SP-EPN 69


title: Tumor 22


title: Normal 23


title: Normal 22


title: Normal 21


title: Tumor 21


title: SP-EPN 68


title: Tumor 20


title: SP-EPN 70


title: SP-EPN 67


title: Normal 19


title: SP-EPN 80


title: Normal 20


title: Tumor 19


title: SP-EPN 51


title: SP-EPN 55


title: SP-EPN 54


title: Tumor 18


title: Normal 18


title: SP-EPN 49


title: Normal 17


title: Tumor 17


title: SP-EPN 48


title: SP-EPN 205


title: Tumor 16


title: SP-EPN 47


title: SP-EPN 46


title: SP-EPN 43


title: Normal 15


title: Normal 16


title: Tumor 14


title: Tumor 15


title: Normal 14


title: SP-EPN 52


title: SP-EPN 39


title: Tumor 13


title: SP-EPN 50


title: Normal 13


title: SP-EPN 38


title: SP-EPN 37


title: Normal 12


title: Tumor 11


title: SP-EPN 34


title: Tumor 12


title: SP-EPN 33


title: SP-EPN 42


title: Tumor 9


title: Tumor 10


title: Normal 9


title: Normal 10


title: SP-EPN 41


title: SP-EPN 29


title: SP-EPN 30


title: Tumor 8


title: SP-EPN 35


title: Normal 8


title: SP-EPN 40


title: SP-EPN 28


title: Tumor 7


title: Normal 7


title: SP-EPN 27


title: SP-EPN 26


title: SP-EPN 24


title: Tumor 6


title: SP-EPN 25


title: Normal 6


title: Normal 11


title: SP-EPN 31


title: Tumor 5


title: SP-EPN 21


title: Normal 5


title: SP-EPN 23


title: SP-EPN 22


title: Normal 4


title: Tumor 4


title: Normal 3


title: Normal 2


title: SP-EPN 16


title: Tumor 3


title: SP-EPN 15


title: Tumor 1


title: SP-EPN 12


title: Tumor 2


title: Normal 1


title: SP-EPN 10


title: 10mT_fractured_2

city: Kanazawa

first: Isao

last: Kobayashi

state: Ishikawa

address: Kakumamachi

country: Japan

institute: Kanazawa University

data_processing:
Illumina RTA software was used for base-calling.
Sequence reads were mapped to the zebrafish reference genome (GRCz11) using BWA-mem (ver. 0.7.17-r1188).
Unique molecular identifier (UMI) counts of each transcript in each sample were calculated using salmon (ver. 1.4.0)
Assembly: GRCz11
Supplementary files format and content: Reads per million (RPM) values for each sample.

source_name: Whole scales

extract_protocol:
Total RNAs were extracted from scales using RNeasy Mini Kit (QIAGEN).
3' RNA-seq was performed according to the Lasy-Seq Ver 1.1 method (Kamitani et al. 2019; Kashima et al. 2022). Total RNA was extracted from zebrafish scales using RNeasy Mini Kit (QIAGEN). Reverse transcription (RT) was performed using Super Script IV (Thermo Fisher Scientific) and an RT primer containing oligo-dT, the index sequence, and 9-bases unique molecular identifiers (UMIs). RNA/cDNA hybrids were purified using AMpure XP beads (Beckman Coulter), and second-strand DNA was synthesized using DNA polymerase I (Enzymatics). dsDNAs were fragmented using WGS Fragmentation Mix (Enzymatics) and ligated into customized adapters with WGS Ligase (Enzymatics). Adapter-ligated dsDNAs were amplified with KAPA HiFi ReadyMix (Nippon Genetics) and SE PCR primers. Next-generation sequencing of cDNA libraries was performed by Novogene using an Illumina NovaSeq X (illumina).

value: Whole scales

value: Wild type

value: Fractured scales exposed to 10 mT ELF-EMFs


title: 10mT_fractured_3


title: 10mT_fractured_1


title: SP-EPN 6


title: 0mT_fractured_2

value: Fractured scales not exposed to ELF-EMFs


title: 0mT_fractured_3


title: 0mT_fractured_1


title: Int_3

value: Intact scales


title: Int_2


title: SP-EPN 1


title: SP-EPN 2


title: Int_1


title: SP-EPN 188


title: SP-EPN 18


title: SP-EPN 19


title: TH_m52

city: Chicago

first: Michihiro

last: Takahama

state: Illinois

department: Pritzker School of Molecular Engineering

institute: University of Chicago

description:
TH, CLP_moderate, d0.5
experiment2
2_counts_CLP_timecourse.txt

data_processing:
We used the RNA-seq pipeline in the bcbio-nextgen project version 1.1.5 (https://bcbio-nextgen.readthedocs.io/en/latest/).
Reads were aligned to the mouse mm10 transcriptomes with RapMap.
Transcripts were counted with fasttagcount in umis (https://github.com/vals/umis).
Quality control metrics were compiled with a combination of FastQC (http:bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (https://github.com/ewels/MultiQC).
Assembly: mm10
Supplementary files format and content: 1_counts_LPS_timecourse.txt: counts matrix from experiment1
Supplementary files format and content: 2_counts_CLP_timecourse.txt: counts matrix from experiment2
Supplementary files format and content: 3_counts_Cytokine_combo.txt: counts matrix from experiment3
Supplementary files format and content: 4_counts_Cytokine_combo2.txt: counts matrix from experiment4
Supplementary files format and content: 5_counts_LPS_Plasma.txt: counts matrix from experiment7
Supplementary files format and content: 6_counts_LPS_KO.txt: counts matrix from experiment9
Supplementary files format and content: 7_counts_LPS_KO2.txt: counts matrix from experiment10
Supplementary files format and content: 8_counts_CLP_timecourse2.txt: counts matrix from experiment11
Supplementary files format and content: 9_counts_CLP_CytoBlock.txt: counts matrix from experiment12
Supplementary files format and content: 10_counts_CLP_CytoBlock2.txt: counts matrix from experiment13
Supplementary files format and content: 11_counts_CLP_antiTNF.txt: counts matrix from experiment14

source_name: Thymus

extract_protocol:
Whole-tissue RNA extraction was performed as described previously (Surya et al., 2020). Briefly, tissues stored in RNA-preserving solution were thawed and transferred to 2 mL tubes containing 700-1500 µL (depending on tissue) of PureZOL (Bio-Rad, 7326890) or homemade Trizol-like solution (38% phenol, 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate, 5% glycerol). Tissues were lysed by adding 2.8-mm ceramic beads (OMNI International, 19-646) and running 1-3 cycles of 5-45 s at 3500 rpm on the PowerLyzer 24 (QIAGEN). For liver, brain, and small intestine samples, tissues were lysed with 3-5 mL using M tubes (Miltenyi biotec, 130-096-335) and running 1-4 cycles of the RNA_02.01 program on the gentleMACS Octo Dissociator (Miltenyi biotec). Next, lysates were processed in deep 96-well plates (USA Scientific 1896-2000) by adding chloroform for phase separation by centrifugation, followed by precipitation of total RNA in the aqueous phase using magnetic beads coated with silane (Dynabeads MyOne Silane; TermoFisher Scientific 37002D), buffer RLT (QIAGEN 79216), and ethanol. Genomic DNA contamination was removed by on-bead DNase I (ThermoFisher Scientific AM2239) treatment at 37 °C for 20 min. After washing steps with 80% ethanol, RNA was eluted from beads. This RNA extraction protocol was performed on the Bravo Automated Liquid Handling Platform (Agilent). Sample concentrations were measured using a Nanodrop One (Termo Scientific). RNA quality was confirmed using a Tapestation 4200 (Agilent Technologies).
For each tissue sample, full-length cDNA was synthesized in 20 µl final reaction volume containing the following: (1) 10 µl of 10 ng/µl RNA; (2) 1 µl containing 2 pmoles of a custom RT primer biotinylated in 5’ and containing sequences from 5’ to 3’ for the Illumina read 1 primer, a 6-bp sample barcode (up to 384), a 10-bp unique molecular identifier (UMI), and an anchored oligo(dT)30 for priming; and (3) 9 µl of RT mix containing 4 µl of 5X RT buffer, 1 µl of 10 mM dNTPs, 2 pmoles of template switching oligo (TSO), and 0.25 µl of Maxima H Minus Reverse Trascriptase (Thermo Scientific, EP0753). First, barcoded RT primers were added to RNA, which were then denatured at 72°C for 1 min and snap cooled on ice. Second, the RT mix was added, and plates were incubated at 42°C for 120 min. For each library, double stranded cDNA from up to 384 samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research, D4013), and residual RT primers were removed using exonuclease I (New England Biolabs, M0293). Full-length cDNAs were amplified with 5 to 8 cycles of single-primer PCR using the Advantage 2 PCR Kit (clontech 639206) and cleaned up using SPRIselect magnetic beads (Beckman Coulter B23318). cDNA was quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific 32851) and 50 ng of cDNA per pool of samples was tagmented using the Tagment DNA Enzyme I (Illumina 20034197) and amplified using the NEBNext Ultra II Q5 Master Mix (NEW ENGLAND BioLabs M0544L). Libraries were gel purified using 2% E-Gel EX Agarose Gels (ThermoFisher Scientific G402002), quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851) and a Tapestation 4200 (Agilent Technologies), and sequenced on the NextSeq 550 platform (Illumina).

value: Thymus


title: TH_m47

description:
TH, CLP_mild, d0.5
experiment2
2_counts_CLP_timecourse.txt


title: TH_m49


title: TH_m46


title: TH_m50


title: TH_m51


title: TH_m48


title: miR1247_P5_rep2

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine

data_processing:
Sequence reads that passed QC filters were mapped to the mm39 mouse genome and transcriptome by Bowtie, and quantified/analyzed using featureCounts from the subread package and DESeq2.
Reads mapping to the miR1247 locus were extracted in BAM file format using SamTool 1.9.
Assembly: mm39
Supplementary files format and content: csv file includes normalized expression values and differential expression analysis by DESeq2 for miR1247 locus for all samples

source_name: RGC

extract_protocol: cDNA libraries prepared using  adaptors that ligate selectively to the endogenously modified 5’ and 3' ends of processed small RNAs, thereby enriching specifically for mature small RNAs, including miRNAs, and excluding degraded RNA fragments, precursors, and other RNA species (TruSeq Small RNA Kit, Illumina). Small RNA cDNA library products in the range of 140-160 base pairs (including 5’ and 3’ adapters and an insert corresponding to a small RNA) were sequenced as paired reads 100 bp from each end on HiSeq 2000 Sequencer (Illumina).

treatment_protocol: Approximately 200,000 of Thy1-immunopanned RGCs were collected (from each condition) and RNA was isolated immediately for preparing cDNA libraries.

tag: strain

value: RGC

value: WT


title: miR1247_P5_rep1


title: TH_m45


title: TH_m44


title: TH_m43


title: SP_m52

description:
SP, CLP_moderate, d0.5
experiment2
2_counts_CLP_timecourse.txt

source_name: Spleen

value: Spleen


title: SP_m51


title: miR1247_E18_rep2


title: miR1247_E18_rep1


title: SP_m49


title: E18_bulk_rep2

data_processing:
Sequence reads that passed QC filters were mapped to the mm39 genome and transcriptome by Hisat2, gene expression was normalized as fragments per kilobase of transcript per million mapped reads (FPKM), and analyzed by Cufflinks/CuffDiff pipeline.
Mapped reads were extracted in BAM file format using SamTool 1.9
Assembly: mm39
Supplementary files format and content: csv file includes FPKM values for gene expression from Cuffdiff for all samples

extract_protocol: cDNA libraries were prepared using polyA-selected RNA (TruSeq RNA Library Prep Kit, Illumina), and paired reads were sequenced 100 bp from each end on HiSeq 2000 Sequencer (Illumina).

treatment_protocol: Adult RGCs transduced with AAV2 expressing miR-1247-5p mimic or scramble shRNA mimic were Thy1-immunopanned from single cell retinal suspension (from 10 retinas per condition) and FACS’ed for mCherry+ cells. Approximately, 5,000 RGCs (per condition) were collected by FACS. Approximately, 50,000 of embryonic day 18 (E18) RGCs were Thy1-immunopanned from single cell retinal suspension.

value: untreated


title: SP_m48


title: E18_bulk_rep1


title: SP_m47

description:
SP, CLP_mild, d0.5
experiment2
2_counts_CLP_timecourse.txt


title: Adult_miR1247_bulk_rep2

value: Adult


title: SP_m50


title: Adult_miR1247_bulk_rep1


title: Th2_12h_Control_5

type: RNA

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

description: US91203659_251485044931_S01_GE1_105_Jan09_1_1

hyb_protocol: After checking the labeling efficiency using the NanoDrop ND-1000 UV–VIS Spectrophotometer, 1.65 µg Cy3 labeled RNA from each sample was hybridized to Agilent Sure-Print G3 Human GE 4 x 44 K slides (Agilent Gene Expression Hybridization Kit).

scan_protocol: standard Agilent  protocol

data_processing: Gene expression data upon Th2 polarization was quantile normalized and log2 transformed    gene expression data were quantile normalized

source_name: Control

label_protocol: 200 ng total RNA was Cy3-labeled using the Agilent Quick Amp Labeling Kit, one color. The labeled cRNA was purified with the RNeasy Mini Kit from Qiagen.

extract_protocol: Human naive CD4+ T cells were isolated from fresh buffy coats with Miltenyis Naïve CD4+ T Cell Isolation Kit II according to the manufacturer’s instructions.

tag: genotype/variation

value: Control


title: Adult_mCherry_bulk_rep2

value: mCherry


title: Th2_12h_knockdown_3

description: US91203659_251485044876_S01_GE1_105_Jan09_1_2


title: LU_m52

description:
LU, CLP_moderate, d0.5
experiment2
2_counts_CLP_timecourse.txt

value: Lung


title: Th2_12h_Control_2

description: US91203659_251485044952_S01_GE1_105_Jan09_1_3


title: SP_m45


title: Th2_12h_knockdown_4

description: US91203659_251485044877_S01_GE1_105_Jan09_1_2


title: Adult_mCherry_bulk_rep1


title: Th2_12h_knockdown_1

description: US91203659_251485044952_S01_GE1_105_Jan09_1_2


title: Th2_12h_Control_3

description: US91203659_251485044876_S01_GE1_105_Jan09_1_1


title: LU_m51


title: SP_m44


title: msCol12

city: Freising

first: Frank

last: Johannes

state: Bavaria

address: Emil-Ramann str. 4

department: Department of Molecular Life Sciences

institute: Technical University of Munich

data_processing:
The clean sRNA data was analysed using Shortstack (Johnson et al., 2016) with default parameters
With “—locifile” we specified intervals (loci) to be analyzed.
As intervals we used 3 set of  200bp regions, based our DNA methylation analysis. One for CG context, one for CHG context and one for CHH context.
As an output in Shortstack there is a "Result: file for each line that has the total number of primary alignments (raw reads) in each locus.
The raw reads for each sample was binded in one total count_table and it is provided here as the processed data file..
Supplementary files format and content: Raw reads counts for each sample using CG regions
Supplementary files format and content: Raw reads counts for each sample using CHG regions
Supplementary files format and content: Raw reads counts for each sample using CHH regions

organism: Arabidopsis thaliana

source_name: Aerial rosette

growth_protocol: The 169 epiRILs were sown in the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) fully automatic phenotyping facility for small plants in long day (16h light, 8h dark ) conditions.

extract_protocol:
Total RNA was extracted from each sample using the miRNeasy kit from Qiagen.
At least 1 μg of total RNA was submitted to the Beijing Genome Institute where they were prepared for Small RNA libraries.

treatment_protocol: Aerial rosette tissue 27 days after sowing (DAS) was harvested.

value: Aerial rosette

tag: line

value: msCol

tag: time

value: Harvested at 27 days after sowing (DAS)


title: 579R

value: epiRil


title: Th2_12h_knockdown_2

description: US91203659_251485044952_S01_GE1_105_Jan09_1_4


title: Th2_12h_Control_1

description: US91203659_251485044952_S01_GE1_105_Jan09_1_1


title: 574F

value: epiHybrid


title: Th2_12h_knockdown_5

description: US91203659_251485044931_S01_GE1_105_Jan09_1_2


title: msCol16


title: 568R


title: 579F


title: SP_m46

value: Wild type


title: 574R


title: LU_m48


title: LU_m46

description:
LU, CLP_mild, d0.5
experiment2
2_counts_CLP_timecourse.txt


title: LU_m47


title: LU_m49


title: Th2_12h_Control_4

description: US91203659_251485044877_S01_GE1_105_Jan09_1_1


title: 539F


title: SP_m43


title: LU_m45


title: 519R


title: 519F


title: 503F


title: 568F


title: LU_m44


title: 503R


title: 469R


title: 467R


title: LI_m51

description:
Li, CLP_moderate, d0.5
experiment2
2_counts_CLP_timecourse.txt

source_name: Liver

value: Liver


title: 469F


title: LI_m49


title: LI_m48


title: LI_m46

description:
LI, CLP_mild, d0.5
experiment2
2_counts_CLP_timecourse.txt


title: 462R


title: LI_m47


title: 539R


title: 462F


title: 454R


title: LI_m50


title: LI_m44


title: 454F


title: LI_m43


title: 426R