title: BW 2 B10

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

data_processing:
Mapping and read counting was conducted using the Salmon mapper and a modified transcriptome, Lie et al 2018
Counts were further normalized using EdgeR
Mapping was conducted with “filtered_Ig_tcr_pigr_transcript.fa” is a modified reference transcriptome based on gene predictions of the wrasse genome (BallGen_V1) published previously in Lie et al 2018, BMC Genomics 19, 186 (2018). https://doi.org/10.1186/s12864-018-4570-8. All fasta transcripts annotated to immunoglobulin genes (IgD, IgT, IgM) and TCR receptors were removed from the previously published transcript file and replaced by curated sequences previously published (Bilal et al 2019, Fish and shellfish Immunology (87), 650-658, https://doi.org/10.1016/j.fsi.2019.02.007)
Assembly: Mapping was conducted with “filtered_Ig_tcr_pigr_transcript.fa” is a modified reference transcriptome based on gene predictions of the wrasse genome (BallGen_V1) published previously in Lie et al 2018, BMC Genomics 19, 186 (2018). https://doi.org/10.1186/s12864-018-4570-8. All fasta transcripts annotated to immunoglobulin genes (IgD, IgT, IgM) and TCR receptors were removed from the previously published transcript file and replaced by curated sequences previously published (Bilal et al 2019, Fish and shellfish Immunology (87), 650-658, https://doi.org/10.1016/j.fsi.2019.02.007)
Supplementary files format and content: Angela_labr_Processed_datafile.txt contains EdgeR-normalized counts.

organism: Labrus bergylta

source_name: Whole larvae

growth_protocol: Brood stock ballan wrasse (30 females and 6 males) were kept in tanks for a year under optimal conditions before the spawning season (beginning of April 2020). After spawning, eggs were collected and placed in incubators until hatching. At 4 dph, 30 000 to 34 000 individuals were transferred into 6 different tanks (B5 – B10) for the feeding trial were three tanks (B6, B8, and B 10) were fed with control diet (rotifers and artemia) and three tanks (B5, B7, and B9) were fed with plankton (2 diets in experimental triplicates). Formulated feed (dry feed) was given at 40 dph for first time in a co-feeding regime until 56 dph were only dry feed was supplied to all the tanks

extract_protocol:
Pooled samples kept in RNA later were thoroughly crushed in a mortar kept at -80°C. Fine powder was collected and used to extract total RNA using a tissue homogenizer (Tissue lyser II) and QIAzol reagent® (Invitrogen) including DNase treatment (TURBO DNase, Ambion) according to the manufacturer’s protocol. For the first sampling point (BW0), TRIzol reagent® (Invitrogen) was used instead. RNA quality was checked using an Agilent 2100 bio-analyser instrument (Agilent technologies, Waldbronn, Germany).
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: Three diets were fed; control diet (rotifers and artemia), Zooplankton and formulated feed (dry feed)

value: Whole larvae

tag: feed group

value: Control

value: 9 days post hatch

tag: tank number

tag: standard length (mm)

tag: sampling stage


title: NCC-HN120P [RHH2232]

status: Public on Feb 17 2023

type: SRA

city: Singapore

first: Yiqun Elaine

last: Cao

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description:
C1 Fluidigm
good_counts.RData
good_tpm.RData
good_cellinfo.RData

library_source: transcriptomic single cell

data_processing:
The raw reads in FASTQ files were aligned to the human genome (hg19 assembly) using STAR v2.6.0
Quantification of gene expression using RSEM v1.3.0 to generate TPM values
Cells with (i) less than 100,000 raw counts, (ii) less than 10% unique exonic mapping rate, or (iii) less than 1,000 expressed genes (TPM > 1) were excluded from analysis
Assembly: hg19
Supplementary files format and content: good_counts.RData is a R data file that contains a data frame of raw read counts for 1,317 cells passing the quality control
Supplementary files format and content: good_tpm.RData is a R data file that contains a data frame of TPM gene expression values for 1,317 cells passing the quality control
Supplementary files format and content: good_cellinfo.RData is a R data file that contains a data frame of cell information for 1,317 cells passing the quality control

molecule: total RNA

organism: Homo sapiens

source_name: tumor

extract_protocol:
Tumors were removed, processed into single cell suspension using a GentleMACS dissociator (Miltenyi Biotec) as described in the manufacturer protocol. Cell suspension were plated and passaged until a tumor majority was observed. On the day of experiment, cancer cell culture were trypsinized and single cell was captured, lysed and reverse transcribed into cDNA using Fluidigm Integrated Fluidic Circuit (IFC) and a Fluidigm C1 instrument (Fluidigm, South San Francisco, CA).
Libraries were prepared for sequencing using C1 Single-Cell Reagent Kit for mRNA Seq

tag: tissue

value: tumor

tag: patient id

tag: primary site

value: L Tongue

tag: lymph node_involved

value: Yes Left Level 1 & Level 2

tag: Stage

tag: grade

tag: site of_origin

value: Primary

tag: cell line

value: patient-derived cell culture

tag: cell type

value: cancer cell


title: NCC-HN120P [RHH2246]


title: NCC-HN120P [RHH2242]


title: NCC-HN120P [RHH2231]


title: NCC-HN120P [RHH2230]


title: NCC-HN120P [RHH2256]


title: BW 2 B5 R3

library_source: transcriptomic

value: Plankton

tag: age


title: BW 2 B8 R3


title: NCC-HN120P [RHH2227]


title: BW 3 B5 R4

value: 18 days post hatch


title: NCC-HN120P [RHH2226]


title: BW 0 R9

value: 4 days post hatch

value: Incubator


title: BW 0 R8


title: NCC-HN120P [RHH2225]


title: NCC-HN120P [RHH2224]


title: BW 0 R6


title: BW 0 R7


title: NCC-HN120P [RHH2222]


title: NCC-HN120P [RHH2228]


title: NCC-HN120P [RHH2223]


title: NCC-HN120P [RHH2219]


title: BW7 B10 R2

value: 80 days post hatch


title: BW7 B9 R2


title: NCC-HN120P [RHH2221]


title: BW7 B9 R1


title: NCC-HN120P [RHH2216]


title: NCC-HN120P [RHH2220]


title: BW7 B7 R2

value: 79 days post hatch


title: NCC-HN120P [RHH2217]


title: BW 3 B5 R3


title: NCC-HN120P [RHH2214]


title: NCC-HN120P [RHH2229]


title: BW7 B10 R1


title: BW7 B8 R2


title: NCC-HN120P [RHH2218]


title: BW7 B8 R1


title: NCC-HN120P [RHH2215]


title: NCC-HN120P [RHH2213]


title: BW7 B6 R2


title: TbRAP1-2FA&5A rep 3

city: CLEVELAND

first: Bibo

last: Li

state: OH

address: 2121 Euclid Avenue

department: Center for Gene Regulation in Health and Disease

country: USA

institute: CLEVELAND STATE University

data_processing:
Base-calling using NovaSeq 6000 for Illumina sequencing
Raw reads were first processed with Novogene Perl Scripts (removing reads with low quality,  with adapters, and containing poly-N; calculating Q20, Q30 and GC contents).
Clean reads were mapped to T. brucei Lister 427 genome TriTrypDB-45_TbruceiLister427_2018_Genome.fasta and its annotation TriTrypDB-45_TbruceiLister427_2018.gff Idownloaded from the TriTryp DB) using HISAT2.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq R package (1.18.0)

molecule: polyA RNA

organism: Trypanosoma brucei brucei

source_name: cultured cells

growth_protocol: Bloodstream form T. brucei cells were cultured in HMI9 medium with 10% FBS. All cells were maintained with medium containing 2 µg/ml G418, 4 µg/ml Hygromycin, 2 µg/ml of Phleomycin, 5 µg/ml blasticidin. TbRAP1F/2FA&5A and TbRAP1F/2FQ cells were also selected with 0.1 µg/ml Puromycin. At the time of adding 100 ng/ml doxycycline, Hygromycin and blasticidin were removed by washing cells 3 times.

extract_protocol:
Total RNA was isolated and purified through RNeasy columns (Qiagen). RNA samples were run on a BioAnalyzer 2100 (Agilent Technologies) using the Agilent RNA 6000 nano kit to verify the RNA quality before sent to Novogene, where RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) using 1 μg poly(A) RNA according to manufacturer’s protocol and index codes were added to attribute sequences to each sample.

treatment_protocol: 100 ng/ml doxycycline (to induce Cre expression) for 30 hrs

tag: genotype

tag: treatment

value: +Cre 30 hrs

tag: strain

value: Trypanosoma brucei brucei lister 427


title: BW7 B6 R1

value: Whole larvae

tag: feed group


title: NCC-HN120P [RHH2211]


title: NCC-HN120P [RHH2208]


title: NCC-HN120P [RHH2209]


title: NCC-HN120P [RHH2207]


title: NCC-HN120P [RHH2210]


title: BW7 B7 R1

tag: tank number


title: TbRAP1-2FA&5A rep 2


title: TbRAP1 CSKO (control for the 2FA&5A mutant) rep S2


title: NCC-HN120P [RHH2206]


title: BW7 B5 R2

tag: standard length (mm)


title: BW7 B5 R1

tag: sampling stage


title: NCC-HN120P [RHH2204]

tag: tissue


title: NCC-HN120P [RHH2205]

tag: patient id


title: TbRAP1-2FQ rep 3


title: NCC-HN120P [RHH2203]

tag: primary site


title: NCC-HN120P [RHH2245]

tag: lymph node_involved


title: TbRAP1-2FQ (F655QF694Q) rep 1


title: NCC-HN120P [RHH2212]

tag: Stage


title: BW6 B10 R2

value: Control

value: 59 days post hatch


title: NCC-HN120P [RHH2201]

value: tumor

tag: grade


title: TbRAP1-2FQ rep 2


title: NCC-HN120P [RHH2202]

value: L Tongue

tag: site of_origin


title: TbRAP1 CSKO (control for the 2FA&5A mutant) rep S1


title: NCC-HN120P [RHH2200]

value: Yes Left Level 1 & Level 2

tag: cell line


title: TbRAP1 CSKO (control for the 2FQ mutant) rep 3


title: NCC-HN120P [RHH2199]

value: Primary

tag: cell type


title: BW6 B10 R1

tag: age


title: TbRAP1-2FA&5A (F655AF694A, 737RKRRR741 mutated to 737AAAAA741) rep 1

tag: genotype


title: NCC-HN120P [RHH2198]

value: patient-derived cell culture


title: NCC-HN120P [RHH2197]

value: cancer cell


title: TbRAP1 CSKO (control for the 2FQ mutant) rep 2

tag: treatment


title: NCC-HN120P [RHH2196]


title: BW6 B8 R2

value: 58 days post hatch


title: TbRAP1 CSKO (conditional single knockout, control for the 2FQ mutant) rep 1

tag: strain


title: NCC-HN120P [RHH2193]


title: BW6 B8 R1

tag: feed group


title: NCC-HN120P [RHH2194]


title: NCC-HN120P [RHH2195]


title: NCC-HN120P [RHH2192]


title: E50, embryo B, part 4, scRNAseq

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

country: China

institute: Zhejiang University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v.6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: calJac4
Supplementary files format and content: h5 files of row counts tables.

organism: Callithrix jacchus

source_name: embryo

extract_protocol: Approximately 1/3 of posterior part of CS12 fetus (Fig XX) were dissociated into single cells with 0.1% Trypsin/EDTA treatment for 15 min at 37 °C with periodic pipetting. After the reaction was quenched by adding an equal volume of FBS strained through a 70 μm nylon cell strainer, cells were resuspended in FACS buffer (0.1% BSA in PBS). Cells were loaded into chromium microfluidic chips with the Chromium Next GEM Single Cell 3ʼReagent Kit (v3.1 chemistry) and then used to generate single-cell gel bead emulsions (GEMs) using the Chromium Controller (10× Genomics) according to the manufacturer’s protocol. GEM-RT was performed in a C1000 Touch Thermal Cycler with 96-Deep Well Reaction Module (Bio-Rad). All subsequent cDNA amplification and library construction steps were performed according to the manufacturer’s protocol. Libraries were sequenced using a 2 × 150 paired-end sequencing protocol on an Illumina HiSeq 4000 or NovaSeq 6000 instrument.

value: embryo

tag: developmental stage

value: embryonic day 50


title: BW6 B9 R2

value: Plankton

tag: tank number

tag: standard length (mm)


title: E50, embryo B, part 3, scRNAseq

tag: tissue


title: BW6 B7 R2

tag: sampling stage


title: NCC-HN120P [RHH2191]

tag: patient id

tag: primary site


title: NCC-HN120P [RHH2190]

tag: lymph node_involved

tag: Stage


title: E50, embryo B, part 2, scRNAseq


title: NCC-HN120P [RHH2189]

tag: grade

tag: site of_origin


title: BW6 B7 R1


title: BW6 B6 R2


title: BW6 B9 R1


title: BW6 B6 R1


title: NCC-HN120P [RHH2186]

tag: cell line

tag: cell type


title: E50, embryo B, part 1, scRNAseq


title: NCC-HN120P [RHH2187]


title: E50, embryo A, part 2, scRNAseq


title: NCC-HN120P [RHH2185]


title: NCC-HN120P [RHH2188]


title: BW6 B5 R2

tag: age


title: NCC-HN120P [RHH2184]


title: NCC-HN120P [RHH2183]


title: E50, embryo A, part 1, scRNAseq


title: BW6 B5 R1


title: BW5 B10 R2

value: 36 days post hatch


title: NCC-HN120P [RHH2182]


title: NCC-HN120P [RHH2180]


title: NCC-HN120P [RHH2179]


title: NCC-HN148M [RHC6580]

value: R retromolar trigone

value: Yes Right Level 2

value: Metastatic (nodal)


title: NCC-HN120P [RHH2178]


title: BW5 B10 R1

value: Whole larvae


title: BW5 B9 R2

value: 41 days post hatch


title: NCC-HN120P [RHH2176]


title: NCC-HN120P [RHH2177]


title: BW5 B9 R1


title: PPC18, post-treatment

city: Portland

first: venkatesh

last: rajamanickam

state: OR

address: 4805 NE Glisan St, Suite 2N35

institute: Earle A. Chiles Research Institute

data_processing:
Expression counts were quantified using salmon-v.0.11.2
Normalization and differential gene expression analysis was conducted using edgeR
Assembly: hg19
Supplementary files format and content: comma separated files include normalized counts for each Sample

source_name: Tumor

extract_protocol:
RNA was extracted and purified using the Qiagen AllPrep DNA/RNA FFPE kit
85ng of input RNA was sequenced using the Illumina TruSeq RNA Exome kit and HiSeq 4000 instrument (2 x 76 reads paired end configuration).

treatment_protocol: pembrolizumab (200mg IV every 3 weeks) with either weekly paclitaxel (80mg/m2 weekly) or fixed-dose capecitabine (2000mg orally twice daily for 7 days of every 14-day cycle) in the 1st/2nd line setting

tag: disease state

value: triple-negative breast cancer

value: Tumor

tag: treatment

value: capecitabine

tag: time

value: post-treatment


title: PPC13, post-treatment

value: paclitaxel


title: PPC05, post-treatment


title: PPC15, post-treatment


title: PPC10, post-treatment


title: PPC27, post-treatment


title: BW5 B7 R1

tag: feed group


title: BW5 B8 R2

value: Control

tag: tank number


title: PPC09, post-treatment


title: BW5 B8 R1

tag: standard length (mm)


title: PPC26, pre-treatment

tag: tissue

value: pre-treatment


title: PPC25, pre-treatment


title: Mouse with forced swim stress [FSS.2]

type: RNA

city: Uchinada-machi

first: HIDEHITO

last: TAKATSUJI

address: Daigaku 1-1

country: Japan

institute: Kanazawa Medical University

description: Gene expression data from hippocampus of mouse with forced swim stress

hyb_protocol: Fragmented and labeled cDNAs were then hybridized onto Affymetrix GeneChip Mouse Gene 1.0 ST arrays in a GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: Arrays were then washed and stained using a GeneChip Fluidics Station 450 and detected using a 3000 7G GeneChip Scanner (Affymetrix).

data_processing: All arrays passed quality control criteria of Expression Console (Affymetrix). Raw data CEL files were then normalized using the RMA algorithm, and data were exported using Expression Console.

label: biotin

organism: Mus

source_name: Hippocampus from mouse with forced swim stress

label_protocol: Subsequently, 300 ng of total RNA was labeled using a GeneChip WT Sense Target Labeling Kit (Affymetrix, Santa Clara, CA, USA) according to manufacturer’s instructions.

growth_protocol: All mice were maintained at a temperature of 21 ± 0.2 ℃ under on constant 12 h light/dark cycles with food and water available ad libitum at Kanazawa medical university.

extract_protocol: The fresh brains were immediately removed from euthanized mice with or without forced swim stress  and were kept in ice-cold PBS for 10 min. The hippocampus tissues dissected from the brain were homogenized in TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH, USA), and total RNA was purified using RNeasy Mini Kit (Qiagen, Hilden, Germany).RNA quality was determined by the ratio of 28S to 18S ribosomal RNA band intensities on electrophoretic gels under denaturing conditions.

treatment_protocol: Forced swim stress was loaded in the following ways. Mice were placed in a glass cylinder containing water 25 ℃ and depth of 25 cm for 11 min daily for 5 consecutive days.

tag: strain

value: 10-11 weeks

value: forced swim stress

value: Hippocampus


title: NCC-HN120P [RHH2181]

value: tumor

tag: patient id

value: L Tongue

value: Yes Left Level 1 & Level 2

value: Primary

value: patient-derived cell culture

value: cancer cell


title: PPC02, post-treatment


title: BW5 B7 R2

value: Whole larvae

value: Plankton

value: 41 days post hatch

tag: sampling stage


title: PPC06, post-treatment

value: triple-negative breast cancer

value: Tumor

value: capecitabine


title: Mouse without forced swim stress [Cont.3]

description: Gene expression data from hippocampus of mouse without forced swim stress

source_name: Hippocampus from mouse without forced swim stress

value: control


title: BW5 B6 R1

value: Control

value: 36 days post hatch


title: Mouse with forced swim stress [FSS.1]

value: 10-11 weeks

value: forced swim stress


title: Mouse without forced swim stress [Cont.2]

value: Hippocampus


title: PPC27, pre-treatment

value: paclitaxel

value: pre-treatment


title: PPC03, post-treatment

value: post-treatment


title: Mouse without forced swim stress [Cont.1]


title: BW5 B6 R2


title: PPC19, pre-treatment


title: Mouse with forced swim stress [FSS.3]


title: BW5 B5 R1


title: Cont.1

description: Gene expression data from hippocampus of mouse without repeated social defeat stress

organism: Mus musculus

source_name: Hippocampus from mouse without repeated social defeat stress

extract_protocol: The fresh brains were immediately removed from euthanized mice with or without repeated socila defeat stress  and were kept in ice-cold PBS for 10 min. The hippocampus tissues dissected from the brain were homogenized in TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH, USA), and total RNA was purified using RNeasy Mini Kit (Qiagen, Hilden, Germany).RNA quality was determined by the ratio of 28S to 18S ribosomal RNA band intensities on electrophoretic gels under denaturing conditions.

treatment_protocol: Repeated social defeat stress was loaded in the following ways. A male B6 mouse was placed with a male ICR mouse in the cage for 10 min daily for 10 days. After the physical contact time,  a male B6 mouse was separeted from a male ICR mouse by white-color board in the cage overnight, so that a male B6 mouse was exposed to various emotional stresses, including visual, auditory, and olfactory stimuli, from a male ICR mouse for 24 hr every day. The pairs of male B6 mice and male ICR mice were randomized daily to minimize the variability in the aggressiveness of male ICR mice. Non-stressed control male B6 mice were placed into each compartment divided by the divider to keep the mice in pairs in the cage and were exchanged the pair every day.

value: 11-12 weeks

value: without repeated social defeat stress


title: Cont.2


title: PPC16, pre-treatment


title: PPC15, pre-treatment


title: PPC18, pre-treatment


title: BW5 B5 R2

value: Whole larvae


title: PPC17, pre-treatment


title: BW4 B10 R2

value: 26 days post hatch


title: RH41TSB

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

description: This file includes hashtag reads from animal replicates of RH4a1_SD3M, RH4b1_SD3M, RH4c1_HFD3M; SD3M: Standard diet 3 month old; HFD3M: High-fat diet 3 month old

library_source: other

data_processing:
RNA readings having a sequence quality of less than 30 from the 10X Chromium platform were filtered out and then mapped to the GRCm38 mouse reference genome using the CellRanger software (version 4.0.0). Seurat v4 was used to read the individual sample output files from CellRanger Count (PMID:31178118). Cells were further filtered out of the downstream analysis using the following criteria: UMI counts per cell, gene counts per cell, and the proportion of transcripts mapped to mitochondrial genes (nFeature RNA > 200 & nFeature RNA > 4000 & percent.mt 1). To detect probable doublets in our data, we used Scrublet (PMID: 30954476), which calculates the chance that a cell is a doublet using barcode and UMI information. Then, we utilized the Seurat function CellCycleScoring to define cell cycle phase and compute G1/S and G2/M phase scores for each cell using a published list of cell cycle genes (PMID: 26430063). SCTransform from Seurat was used to independently normalize the gene-cell count matrices, with the "vars.to.regress" parameter set to the proportion of mitochondrial genes, cell cycle score, and default values for other parameters (PMID: 31870423). Finally, using the Seurat SCTransform integration procedure, the datasets were combined.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: other

source_name: Hippocampal microglia

extract_protocol:
We performed a papain enzymatic digestion followed by serial trituration to prepare a single cell suspension from the hippocampus. We enriched for microglia by applying a 40% Percoll centrifugation to our cells and collecting the cell pellet, and further purified by fluorescence activated cell sorting (FACS). We sorted CD11b+/CD45low double positive cells, representing microglia, rather than CD11b+/CD45high cell surface markers, which represent macrophages.
scRNA-seq was performed by the Advanced Genomics Core at the University of Michigan using the 10X Genomics Chromium system (10X Genomics): An automated counter (Countess II, Thermo Fisher) was used to quantify cells/µl. The single cell suspension was then diluted to a final concentration ranging from 700 to 1000 cells/µl. Using the Chromium Controller, 3’ libraries of single cells were created leveraging 3’ V3.1 chemistry using NextGEM Chip G reagents, according to the manufacturer’s protocol (all from 10X Genomics). The quality of the final library was evaluated by Tapestation 4200 (Agilent) and Kapa qPCR (Roche) was used to quantify libraries. Pooled libraries were sequenced using 150 bp paired-end format (Illumina NovaSeq 6000). De-multiplexed Fastq files were generated (Bcl2fastq2 Conversion Software, Illumina) and reads were aligned and counted (CellRanger Pipeline, 10X Genomics).

value: Hippocampal microglia

value: 3 month


title: PPC14, pre-treatment

value: triple-negative breast cancer

value: Tumor


title: R-SDS.1

description: Gene expression data from hippocampus of mouse with repeated social defeat stress

source_name: Hippocampus from mouse with repeated social defeat stress

value: with repeated social defeat stress


title: PPC13, pre-treatment


title: RH32TSB

description: This file includes hashtag reads from animal replicates of RH3a2_HFD3M, RH3b2_SD3M, RH3c2_HFD3M; SD3M: Standard diet 3 month old; HFD3M: High-fat diet 3 month old


title: BW4 B10 R1

value: Control


title: RH31TSB

description: This file includes hashtag reads from animal replicates of RH3a1_SD3M, RH3b1_HFD3M, RH3c1_SD3M; SD3M: Standard diet 3 month old; HFD3M: High-fat diet 3 month old


title: BW4 B9 R2

value: Plankton

value: 28 days post hatch


title: R-SDS.2


title: RH21TSB

description: This file includes hashtag reads from animal replicates of RH2a1_SD1M, RH2b1_SD1M, RH2c1_HFD1M; SD1M: Standard diet 1 month old; HFD1M: High-fat diet 1 month old

value: 1 month


title: PPC12, pre-treatment


title: BW4 B8 R2


title: BW4 B9 R1


title: PPC10, pre-treatment

value: capecitabine


title: BW4 B8 R1


title: RH12TSB

description: This file includes hashtag reads from animal replicates of RH1a2_SD1M, RH1b2_HFD1M, RH1c2_HFD1M; SD1M: Standard diet 1 month old; HFD1M: High-fat diet 1 month old


title: RH42TSB

description: This file includes hashtag reads from animal replicates of RH4a2_SD3M, RH4b2_HFD3M, RH4c2_HFD3M; SD3M: Standard diet 3 month old; HFD3M: High-fat diet 3 month old


title: RH11TSB

description: This file includes hashtag reads from animal replicates of RH1a1_SD1M, RH1b1_SD1M, RH1c1_HFD1M; SD1M: Standard diet 1 month old; HFD1M: High-fat diet 1 month old


title: PPC09, pre-treatment


title: PPC08, pre-treatment

value: paclitaxel


title: RH42

description: This file includes cells from animal replicates of RH4a2_SD3M, RH4b2_HFD3M, RH4c2_HFD3M; SD3M: Standard diet 3 month old; HFD3M: High-fat diet 3 month old


title: BW4 B7 R1


title: PPC06, pre-treatment

value: pre-treatment


title: RH22TSB

description: This file includes hashtag reads from animal replicates of RH2a2_SD1M, RH2b2_HFD1M, RH2c2_HFD1M; SD1M: Standard diet 1 month old; HFD1M: High-fat diet 1 month old


title: RH41

description: This file includes cells from animal replicates of RH4a1_SD3M, RH4b1_SD3M, RH4c1_HFD3M; SD3M: Standard diet 3 month old; HFD3M: High-fat diet 3 month old


title: RH32

description: This file includes cells from animal replicates of RH3a2_HFD3M, RH3b2_SD3M, RH3c2_HFD3M; SD3M: Standard diet 3 month old; HFD3M: High-fat diet 3 month old


title: PPC05, pre-treatment


title: BW4 B7 R2


title: BW4 B6 R2


title: PPC04, pre-treatment


title: RH22

description: This file includes cells from animal replicates of RH2a2_SD1M, RH2b2_HFD1M, RH2c2_HFD1M; SD1M: Standard diet 1 month old; HFD1M: High-fat diet 1 month old


title: PPC03, pre-treatment


title: oBHV replicate 5

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St W

department: Medicine

country: Canada

institute: McMaster University

hyb_protocol: Fragmented sample was hybridized to Affymetrix Clariom S arrays at 45 °C overnight.

scan_protocol: Arrays were imaged using GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Data was analyzed using the Transcriptome Analysis Console software, Thermo Fischer. Data was processed using RMA, Quantile Normalization, HDF5 output.

label: Biotin

source_name: B16-C10 subcutaneuos tumour from C57Bl/6 mouse

label_protocol: RNA was normalized to an input amount of 100 ng and underwent reverse transcription. sscDNA was purified using magnetic beads and fragmented using UDG

growth_protocol: 6- to 8-week-old C57Bl/6 mice were subcutaneously implanted with 5 × 106 B16-C10 cells resuspended in 200 µL PBS into the left flank

extract_protocol: Mice were sacrificed and tumours harvested at day 5. Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by further purifying using the Qiagen RNA extraction kit (Cat #74004)

treatment_protocol: At 2 weeks post-injection: for MMC therapy, tumors were treated intratumorally (i.t.) with 100 µg MMC in 50 µL sterile water only at day 1. For oBHV therapy, tumors were treated i.t. by injecting 2 × 107 pfu oBHV in 50 μL PBS beginning at day 2 once daily for 3 consecutive days (days 2, 3 and 4)

value: B16-C10 subcutaneuos tumour

value: oBHV


title: PPC02, pre-treatment


title: oBHV replicate 4


title: RH21

description: This file includes cells from animal replicates of RH2a1_SD1M, RH2b1_SD1M, RH2c1_HFD1M; SD1M: Standard diet 1 month old; HFD1M: High-fat diet 1 month old


title: oBHV replicate 2


title: BW3 B10 R2

value: 16 days post hatch


title: oBHV replicate 3


title: BW4 B5 R2

value: Whole larvae


title: BW4 B5 R1


title: PPC01, pre-treatment


title: RH11

description: This file includes cells from animal replicates of RH1a1_SD1M, RH1b1_SD1M, RH1c1_HFD1M; SD1M: Standard diet 1 month old; HFD1M: High-fat diet 1 month old


title: BW3 B10 R1


title: BW3 B9 R2

value: 18 days post hatch


title: H7iE9_stim_3

city: Philadelphia

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

data_processing:
Base calling
Data filtering/QC was performed with bbduk
Psuedoalignment and transcript quantification was performed with Salmon
Differential gene expression analysis was carried out using DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample.

source_name: HDAC7iE9 cells, stimulated

growth_protocol: Jurkat T cells (JSL1 clone) were cultured in RPMI 1640 supplemented with 5% heat-inactivated fetal bovine serum, penicillin and streptomycin (100 units/mL each), and grown at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted using RNA-STAT (Tel-Test) following manufacturer’s protocol.
PolyA selection, library preparation and sequencing was performed by Azenta Life Sciences (formerly Genewiz).

treatment_protocol: All cell lines were grown in unstimulated or stimulated conditions (20 ng/mL phorbol 12-myristate 13-acetate, PMA) for 48 hours prior to harvest.

value: JSL1 HDAC7 E9+

value: Jurkat T cells

tag: genotype

value: HDAC7 E9 knock-in

value: PMA stimulation

value: 48 hours


title: H7iE9_stim_1


title: H7iE9_unstim_3

source_name: HDAC7iE9 cells, unstimulated

value: growth medium


title: BW3 B9 R1

value: Plankton


title: BW3 B8 R2

value: Control


title: RH31

description: This file includes cells from animal replicates of RH3a1_SD3M, RH3b1_HFD3M, RH3c1_SD3M; SD3M: Standard diet 3 month old; HFD3M: High-fat diet 3 month old

value: Hippocampal microglia

value: 3 month


title: BW4 B6 R1

value: 26 days post hatch


title: H7iE9_stim_2


title: H7iE9_unstim_2


title: Sorted LT-HSC 15417

city: Bonn

first: Amir Hossein

last: Kayvanjoo

address: Carl-Troll-Straße 31

country: Germany

institute: LIMES Institute

data_processing:
Samples were demultiplexed and fastq files were generated using bcl2fastq2 v2.20 before alignment and quantification using Kallisto v0.44.0 based on  the Gencode (mm10, GRCm38) vM16 (Ensembl 91) reference genomes.
Sequencing results  from the experiments were pseudoaligned using the Kallisto tool set
The final count matrix is free of GM, Rik, LOC, and sex genes.
Assembly: mm10
Supplementary files format and content: tab-separted value files, comma-separted value file for the final proccessed counts

source_name: Primary

extract_protocol:
RNA was extracted using the miRNeasy micro kit (Qiagen) and quantified via RNA assay on a tape station 4200 system (Agilent)
RNA was used as an input for library generation via SmartSeq 2 (SS2) RNA library production protocol as previously described (Picelli et al., 2014)

value: Primary

value: LT-HSC

value: Tnfrsf11a+/+; Spi1f/f

tag: developmental stage


title: Sorted LT-HSC 15420


title: Sorted LT-HSC 15418


title: Sorted LT-HSC 15416


title: H7iE9_unstim_1


title: BW3 B7 R2


title: BW3 B8 R1

value: 16 days post hatch


title: RH12

description: This file includes cells from animal replicates of RH1a2_SD1M, RH1b2_HFD1M, RH1c2_HFD1M; SD1M: Standard diet 1 month old; HFD1M: High-fat diet 1 month old

value: 1 month


title: Sorted LT-HSC 15412

value: Tnfrsf11aCre; Spi1f/f


title: H7dE9_stim_2

source_name: HDAC7dE9 cells, stimulated

value: JSL1 HDAC7 E9-/-

value: HDAC7 E9 knock-out


title: Sorted LT-HSC 15415


title: Sorted LT-HSC 15411


title: H7dE9_stim_3

value: Jurkat T cells


title: BW3 B6 R2

value: Whole larvae


title: BW3 B7 R1

value: 18 days post hatch


title: H7dE9_stim_1

value: PMA stimulation

value: 48 hours


title: H7dE9_unstim_3

source_name: HDAC7dE9 cells, unstimulated

value: growth medium


title: H7dE9_unstim_2


title: Sorted LT-HSC 15406


title: BW3 B6 R1

value: Control


title: Sorted LT-HSC 15409


title: oBHV replicate 1

value: B16-C10 subcutaneuos tumour

value: oBHV


title: BW2 B10 R1

value: 9 days post hatch


title: Sorted LT-HSC 15405

value: Primary

value: LT-HSC


title: JSL1_stim_2

source_name: JSL1 cells, stimulated

value: WT


title: BW2 B8 R2

source_name: Whole larvae


title: BW2 B9 R2

value: Plankton


title: Dbia_69-Pupa_bioRep-2

city: Planegg-Martinsried

first: Nicolas

last: Gompel

address: Grosshaderner Str. 2

department: Faculty of Biology

institute: Ludwig Maximilian University of Munich

library_source: genomic

data_processing:
ATAC-seq libraries were processed as described (GSE142176; doi: 10.1073/pnas.2004003117):  The sequenced libraries were demultiplexed, trimmed, and aligned to the reference genome UCSC dm6 using Bowtie2 with following settings: -X 2000; --fr; --very-sensitive.
The aligned reads were then filtered by Picard with the following steps: clean sam, FixMate information, MarkDuplicate. The PCR duplicates were subsequently removed by SAMtools.
BigWig files were converted from normalized bedGraph files, which were generated by MACS2 with following settings: --keep-dup all; -q 0.01; --nomodel; --shift -100; --extsize 200.
Peaking calling was performed using HOMER with following settings: -style histone -size 100 -minDist 100 -gsize 1.2e+8 -o auto.
Assembly: dm6 for D. melanogaster; GCF_000233415.1 for D. biarmipes
Supplementary files format and content: BigWig files for normalized signal track, bed files for peaks called by HOMER.

molecule: genomic DNA

organism: Drosophila biarmipes

source_name: Pupal wings

growth_protocol: The Drosophila genome lines used in this study were maintained on standard cornmeal medium at 20ºC with a 12:12 day-night light cycle.

extract_protocol:
Nuclei were extracted and prepared as described before (GSE142176) with some modifications: dissected wings were immediately moved into cold 1x lysis buffer after rinsing. 24 0% pupal development wing discs, 14-17 wings from at least 11 individuals at 47% pupal development, and 24 wings from later stages were used for following steps, respectively. Only the pupal wings older than 60% of pupal development were cut before disruption. Samples were incubated on ice for 20-30 min before and after disruption. For tagmentation: the reaction was set up with 18 µl of Tagment DNA Buffer (Illumina #15027866) with nuclei, plus 2 µl of Tagment DNA Enzyme (Illumina #15027865).
ATAC-seq libraries were prepared as described before (GSE142176; doi: 10.1073/pnas.2004003117).  The libraries were amplified by NEBNext High-Fidelity 2X PCR Master Mix (NEB Cat. M0541S) for 9-11 PCR cycles, purified by Agencourt AMPure XP beads (Beckman Coulter) with double size selection (0.5x and 2.0x), and validated by Bioanalyzer using High Sensitive DNA chip (Agilent).

value: Pupal wings

value: 69% of pupal development

tag: Sex

value: Male


title: H7dE9_unstim_1

value: JSL1 HDAC7 E9-/-

value: Jurkat T cells

value: HDAC7 E9 knock-out


title: BW2 B9 R1

value: Whole larvae


title: Dbia_48-Pupa_bioRep-2

value: 48% of pupal development


title: BW2 B7 R1


title: ccf-1 acrylamide2

city: Saskatoon

first: Cheng-Wei

last: Wu

state: SK

address: 52 Campus Drive

institute: University of Saskatchewan

data_processing:
HISAT2 v2.0.5 used for mapping to the C. elegans reference genome
FeatureCounts v1.5.0-p3 used for Quantification
StringTie v1.3.3 used for novel gene prediction.
DESeq2 v1.20.0 used for differential expression analysis
Genome_build: wbcel235
Supplementary_files_format_and_content: tab-delimited text files include differential gene expression

organism: Caenorhabditis elegans

source_name: whole animal

extract_protocol:
Total RNA extracted using the RNAqueous Total RNA Isolation Kit
Standard Illumina protocols with oligo-dT beads

value: acrylamide (5mM 24h)

value: ccf-1 RNAi


title: ccf-1 acrylamide3


title: JSL1_unstim_1

source_name: JSL1 cells, unstimulated

value: growth medium

value: 48 hours


title: BW2 B6 R2

value: Control

value: 9 days post hatch


title: Dbia_78-Pupa_bioRep-2

value: 78% of pupal development


title: ccf-1 acrylamide1


title: RHT5555

data_processing:
The scRNA-seq reads were aligned to the GRCh38 reference genome and quantified using cellranger count
For clustering of all cell types, Seurat integration was applied across patients to reduce patient specific effects
Clusters were identified using shared nearest neighbor (SNN)-based clustering
Cell types were annotated using the resulted DE genes together with the expression of known marker genes
Genome_build: GRCh38
Supplementary_files_format_and_content: R data of Seurat object containing UMI counts, normalized data and cell type information

source_name: Head and neck squamous cancer

extract_protocol:
Tumors were removed, processed into single cell suspension using a GentleMACS dissociator (Miltenyi Biotec) as described in the manufacturer protocol. Single cell was captured, lysed and reverse transcribed into cDNA using Fluidigm Integrated Fluidic Circuit (IFC) and a Fluidigm C1 instrument (Fluidigm, South San Francisco, CA), and the 10x Chromium Single Cell V(D)J Reagent Kits and 10x Chromium controller, as described in the manufacturer protocols.
Libraries were prepared for sequencing using C1 Single-Cell Reagent Kit for mRNA Seq and 10x Chromium Single Cell V(D)J Reagent Kits

value: HN263 Met

tag: tumor origin

value: Metastatic lymph node


title: JSL1_stim_1

tag: cell line

value: WT

value: PMA stimulation


title: Dbia_60-Pupa_bioRep-2

value: Pupal wings

value: 60% of pupal development

value: Male


title: Dbia_78-Pupa_bioRep-1


title: RHT5551

value: HN263 Pri

value: Primary


title: JSL1_unstim_2

tag: cell type

value: Jurkat T cells


title: BW0 R 3

value: Whole larvae

tag: age

value: 4 days post hatch

value: Incubator


title: Dbia_0-Pupa_bioRep-2

value: 0% of pupal development


title: Dbia_60-Pupa_bioRep-1


title: BW2 B5 R1

value: Plankton


title: ccf-1 cadmium3

value: cadmium (100uM 24h)

value: ccf-1 RNAi


title: RHT5543

value: HN257 Pri


title: Dbia_69-Pupa_bioRep-1

value: 69% of pupal development


title: ccf-1 cadmium1


title: RHT5539

value: HN251 Met

value: Metastatic lymph node


title: RHT5547

value: HN257 Met


title: Dbia_0-Pupa_bioRep-1

value: Pupal wings


title: BW2 B6 R1

value: Control

value: 9 days post hatch


title: ccf-1 control3

value: control


title: jejunum,transport,rep2

city: Harbin

first: Honggui

last: Liu

address: changjiang street num 600

institute: Northeast Agricultural University

description: healthy

data_processing:
counts and fpkm
Supplementary files format and content: excel,expression profiles

organism: Sus scrofa

source_name: Weaned piglets

growth_protocol: jejunum tissues were maintained in RNase-free EP tubes at -80C

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
RNA libraries were prepared for sequencing using standard Illumina protocols

value: jejunum

tag: breed

value: Large WhitexLandrace

value: transport


title: ccf-1 control2

tag: treatment


title: C57BL/6 Mouse Lung, PR8 + 2

city: Fuzhou

first: JiLong

last: Chen

address: Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University

data_processing:
Data preprocessing and genomic alignment. Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads. Using hisat2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
CircRNA prediction, Expression analysis and Interaction research. In order to generate SAM file, we used BWA software to align the sequencing reads of each sample with reference genome. Then CIRI software was used to scan for PCC signals (paired chiastic clipping signals), and circRNA sequences were predicted based on junction reads and GT-AG cleavage signals.
Using the RPM algorithm to quantify the circRNAs, and normalizing the number of junction reads counts and foldchange by DESeq. Enrichment of differentially expressed circRNAs was analysised through the annotation information of circRNA source transcripts.
Read count extraction and normalization were performed using CLC genomic benchwork
Gene structure optimization and New transcript prediction. Comparing the merged transcripts with the gene annotation information of the reference sequence through Cuffcompare, assembled transcripts would be lengthened during 5’ or 3’region. It could be considered as optimization of the gene structure. Comparing the new annotation information and known annotation information to obtain new transcript information. With the above comparison results, new transcript predictions could be performed at the same time. Assembly results must satisfy the following conditions to be considered as new transcripts: 200 bp or more apart from the existing annotation gene; and not less than 180 bp in length.
Supplementary files format and content: mm10
Supplementary files format and content: counts, fpkm

source_name: Lung

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or other platform) and 150 bp/125bp paired-end reads were generated.
TruSeq Stranded Total RNA with Ribo-Zero Gold

value: Lung

value: Lung cells

value: WT

value: 1x10^4 PFU/ml of IAV PR8


title: RHT5531

value: HN242 Met


title: BW2 B7 R2

value: Whole larvae

value: Plankton


title: ccf-1 cadmium2

value: cadmium (100uM 24h)

value: ccf-1 RNAi


title: C57BL/6 Mouse Lung, PR8 + 1

department: Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences

institute: Fujian Agriculture and Forestry University


title: C57BL/6 Mouse Lung, PR8 + 3


title: Dbia_48-Pupa_bioRep-1

value: 48% of pupal development

value: Male


title: C57BL/6 Mouse Lung, PR8 - 1

value: Mocked


title: C57BL/6 Mouse Lung, PR8 - 2


title: ccf-1 control1


title: C57BL/6 Mouse Lung, PR8 - 3


title: Ev acrylamide3

value: acrylamide (5mM 24h)

value: wildtype


title: RHT5535

value: HN251 Pri

value: Primary


title: jejunum,transport,rep1

description: healthy

value: jejunum

value: Large WhitexLandrace

value: transport


title: WT 3_ EB_d5

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

hyb_protocol: Bisulfite conversion and hybridization to the array was carried out by Life&Brain (Bonn, Germany). Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium EPIC Beadchip using the standard protocol from Illumina.

scan_protocol: Standard protocol from Illumina.

data_processing: Analysis was performed on RAW idat files using the R package minfi and the ssNoob normalization. Detection p values were calculated using the SeSAMe package and the pOOBAH approach.

label: Cy5 and Cy3

source_name: EB

label_protocol: Standard protocol from Illumina.

growth_protocol: The iPSC lines were cultured on tissue culture plastic coated with vitronectin (0.5 µg/cm2) in StemMACS iPS-Brew XF (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). EBs were generated with a micro-contact printing (µCP) approach published in (). Multilineage differentiation of EBs was performed with differentiation induction medium (EB-medium) containing Knockout DMEM (Gibco, Carlsbad, USA), 20 % v/v FCS (Lonza, Basel, Switzerland), 2 mM L-Glutamine, 1x Non-Essential amino acids, 100 nM b-Mercaptoethanol, and 100 U/mL Penicillin/Streptomycin solution. EBs were differentiated in ultra-low attachment plates (Corning, New York, USA) for 5 days.

extract_protocol: Genomic DNA was isolated with the NucleoSpin Tissue Kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: Directed differentiation toward endodermal, mesodermal, and ectodermal lineage was induced with the STEMdiff Trilineage Differentiation Kit (Stemcell Technologies, Vancouver, Canada).

tag: gender

value: male

tag: differentiation timepoint

tag: sample group

value: Day 5 EB

value: EB

value: WT


title: YAP-/- 1_EB_d5

value: female

value: Day 5 EB KO

value: YAP-/-


title: KO3

city: Nashville

first: Justin

last: Jacobse

state: Tennessee

address: 2215 Garland Avenue

institute: Vanderbilt University Medical Center

data_processing:
Samples were trimmed with fastp (version 0.20.0) using default parameters. Quantification was performed using Salmon (version 1.4.0) against a decoy transcriptome (Mus musculus Gencode version 21)
Further analysis was performed in R (version 4.1.2) in R studio (version 2021.09.2+382) based on a pipeline described by Love et al. (2019).
Quantification files were imported with tximeta (version 1.2.2) and genes with counts £1 were omitted. Normalization was performed for principal component analysis and gene clustering plots with variance stabilizing transformation and regularized-logarithm transformation, respectively.
Differential expression analysis was performed on non-normalized counts using DESEq2 (version 1.34.0).
Annotation was done with AnnotationDbi (version 1.56.2) using org.Mm.eg.db (version 3.14.0).
Assembly: Mus musculus Gencode version 21
Supplementary files format and content: Absolute and DE-seq2 normalized counts.

source_name: colonic lamina propria

extract_protocol:
The RNAeasy Micro Kit (Qiagen) was used, and cells were sorted directly into 300 mL RLT buffer containing 2-mercapto-ethanol as recommended.
RNA amplification using the Ovation RNASeq System V2 kit, cDNA library preparation using the NEB library kit

value: colonic lamina propria

value: flow-sorted live CD45+CD4+Foxp3+ cells

value: no treatment

tag: batch flow_sort

value: D

tag: rna integrity_number_(rin)


title: EV cadmium3

value: cadmium (100uM 24h)

value: wildtype


title: RHT5527

value: HN242 Pri

value: Primary


title: Ev acrylamide2

value: acrylamide (5mM 24h)


title: jejunum,transport,rep3

description: healthy

tag: tissue

value: jejunum

value: Large WhitexLandrace

value: transport


title: iPSC YAP-/- 2_ECTO

description: iPSC 102 #30 ECTO

source_name: iPSC

value: ectoderm

value: iPSC


title: EV cadmium2


title: jejunum,control,rep1

description: healthy

value: No transport


title: iPSC YAP-/- 2_MESO

description: iPSC 102 #30 MESO

value: female

value: mesoderm


title: WT 1_ EB_d5

value: Day 5 EB

value: EB

value: WT


title: Mouse_Liver_Array_4_pool_c

description: Seq-Well

data_processing:
Fastq files from Seq-Well were loaded into a snakemake-based data pre-processing pipeline (version 0.31, available at https://github.com/Hoohm/dropSeqPipe)
STAR alignment within the pipeline was performed using the murine GENCODE reference genome and transcriptome mm10 release vM16
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Fetal liver

extract_protocol:
The fetal liver was collected from wild-type mouse embryos. The collected tissues were digested for 20 min at 37 °C in a digestion solution. The cell suspensions were centrifuged and the supernatants were removed. The pellets were resuspended, washed and stained for 25 min. Finally, the pellet was resuspended in FACS buffer. The CD11blow/+ F4/80+ cells were sorted into microtubes containing FACS buffer.
Seq-Well arrays were prepared as described by Gierahn et al. (Gierahn, Wadsworth et al. 2017).
Seq-Well libraries were generated as described by Gierahn, Wadsworth et al. 2017 and Hughes, Wadsworth et al. 2020.

value: Fetal liver

tag: strain


title: iPSC YAP-/- 2_ENDO

description: iPSC 102 #30 ENDO

value: endoderm

value: YAP-/-


title: MUX9220

tag: patient id

value: HN279 Pri


title: Ev acrylamide1

tag: genotype

value: wildtype


title: RHT5523

value: HN237 Met

value: Metastatic lymph node


title: jejunum,control,rep3

description: healthy

value: jejunum

value: Large WhitexLandrace


title: iPSC YAP-/- 1_ECTO

description: iPSC 102 #20 ECTO

value: ectoderm


title: EV control 3 (cadmium and acrylamide control)

value: control


title: iPSC YAP-/- 1_ENDO

description: iPSC 102 #20 ENDO

value: iPSC


title: iPSC YAP-/- 2_ SC

description: iPSC 102 #30 undifferentiated

value: female

value: undifferentiated


title: MUX8651

value: HN272 Pri

value: Primary


title: YAP-/- 2_EB_d5

value: Day 5 EB KO

value: EB


title: RHT5519

value: HN237 Pri


title: EV control 2 (cadmium and acrylamide control)


title: Mouse_Liver_Array_4_pool_a

description: Seq-Well

value: Fetal liver

tag: developmental stage


title: MUX9221

value: HN279 Met


title: iPSC YAP-/- 1_SC

description: iPSC 102 #20 undifferentiated

value: YAP-/-


title: jejunum,control,rep2

description: healthy

value: No transport


title: Mouse_Liver_Array_3_pool_c

description: Seq-Well


title: KO2

value: colonic lamina propria

value: flow-sorted live CD45+CD4+Foxp3+ cells

value: no treatment

value: C


title: EV control 1 (cadmium and acrylamide control)

value: control

value: wildtype


title: Mouse_Liver_Array_4_pool_b

description: Seq-Well


title: MUX8652

value: HN272 Met

value: Metastatic lymph node


title: WT 2_ EB_d5

value: female

value: Day 5 EB

value: WT


title: Mouse_Liver_Array_3_pool_b

description: Seq-Well


title: LPS5

city: new haven

first: Kristopher

last: Kahle

state: CT

address: 333 ceder st

department: Department of Neurosurgery

institute: Yale university

data_processing:
Expression level for each gene was estimated using Python program HTSeq (https://academic.oup.com/bioinformatics/article/31/2/166/2366196).
Htseq-count function of HTSeq accumulated the number of aligned reads that falls under the exons of the gene.

organism: Rattus norvegicus

source_name: choroid plexus (ChP)

extract_protocol:
Immediately following transcardial perfusion with ice cold TBS (pH = 7.60), the brain was isolated and placed in an ice-cold saline bath. Brains were cut sagittally along the interhemispheric line to expose the lateral ventricles, and choroid plexuses were rapidly but carefully dissected from both lateral ventricles using sharp forceps under magnification. Each brain yielded ~3 mg of choroid plexus tissue total, which was collected into a 1.5 mL tube, snap frozen in liquid nitrogen, and stored at -80oC until use.
Full length high quality total cell RNA isolated by Qiagen RNAeasy micro kit (Quigen, https://www.qiagen.com/us/shop/pcr/rneasy-micro-kit/). ChP cells were homogenized in 350ul RLT buffer with beta-mercaptoethanol in Tissuelyzer for 10 mins and proceed according to the instructions in RNAeasy Micro RNA kit and RNAs was eluted in 18ul dH2O. 16ul of elutant was recovered and 1.2ul was used for the QC. Libraries were run on an Illumina HiSeq 2500 at the Yale Center for Genome Analysis. The R/Bioconductor package “DESeq2” was used to identify differentially expressed genes between cell populations derived from control, IVH-treated and LPS-treated rats (Love et al., 2014). Genes with a log2-fold change expression greater than 3 and a q-value less than 0.01 were considered significant. The R ComplexHeatmap package was used to visualize the heatmap expression of highly variable genes (Gu et al., 2016). Volcano plots were generated using the R package EnhancedVolcano (Blighe et al., 2019).

treatment_protocol: LPS/IVH 48 hhs ICV

value: LPS-Treated


title: iPSC YAP-/- 1_MESO

description: iPSC 102 #20 MESO

value: mesoderm

value: iPSC


title: LPS4


title: KO1

value: A


title: MUX8293

value: HN263 Met


title: XHC028

value: HN251 Met


title: EV cadmium1

value: cadmium (100uM 24h)


title: Mouse_Liver_Array_2_pool_b

description: Seq-Well

value: Fetal liver


title: Mouse_Liver_Array_2_pool_a

description: Seq-Well


title: WT3

value: colonic lamina propria

value: flow-sorted live CD45+CD4+Foxp3+ cells

value: no treatment

value: B


title: LPS1


title: WT2


title: Mouse_Liver_Array_3_pool_a

description: Seq-Well


title: LPSControl5

value: Untreated


title: WT1


title: MUX8290

value: HN263 Pri

value: Primary


title: LPS2


title: XHH002

value: HN257 Met

value: Metastatic lymph node


title: XHC027

value: HN251 Pri


title: XHH001

value: HN257 Pri


title: LPSControl4


title: MUX6681

value: HN237 Met


title: Mouse_Liver_Array_2_pool_c

description: Seq-Well


title: Mouse_Liver_Array_1_pool_a

description: Seq-Well


title: LPSControl2


title: XHC025

value: HN242 Pri


title: Mouse_Liver_Array_1_pool_c

description: Seq-Well


title: LPSControl3


title: Mouse_Liver_Array_1_pool_b

description: Seq-Well


title: KO1_S3_L_scRNA-seq

city: Mexico city

first: Aarón

last: Vázquez-Jiménez

state: Mexico city

address: Periferico Sur 4809

country: Mexico

institute: INMEGEN

data_processing:
In order to process single cell mRNA sequencing data, we generated the count expression matrixes by aligning the raw data to the mouse genome (GRCm38.98) following previous reports ( Romagnoli et al., 2018; Tian,L et al, 2018), using the default parameters.
Genome_build: GRCm38.98
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: C56BL/6J (Stra8-iCre-Ctcf f/Δ )

extract_protocol:
Testes were removed. Then an enzymatic and mechanically digestion was made to obationed a cell supension. We performed single cell isolation and cell barcoding with the Droplet-based Single-cell isolator (one-touch ddSEQ, Bio-Rad) according to the manufacturer’s instructions.
Single-cell-barcoded RNA-Seq libraries using Nextera technology included in the SureCell WTA 3′ Library Prep Kit (Illumina). Next generation sequencing was performed in a NextSeq (Illumina) with an attainable depth of 250,000 reads/cell

tag: background strain

value: 15 weeks old

value: Ctcf-cKO

value: testes


title: IVH5

value: IVH-Treated


title: KO3_S4_L_scRNA-seq


title: XHC026

city: Singapore

first: Yiqun Elaine

last: Cao

address: 8 College Road

institute: Duke-NUS Medical School

value: HN242 Met

tag: tumor origin


title: WT2_S2_L_scRNA-seq

source_name: C56BL/6J (Ctcf wt/wt)

value: Wild Type


title: IVH2


title: Rat; isoproterenol (5 mg/kg/d),10 days; exercised (60min/d), 4weeks. [113]

city: Jinan

first: Bingyu

last: Du

state: 请选择省

address: Jingshi Road

institute: 山东省千佛山医院

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the GRnor_6.0.100 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Assembly: GRnor_6.0.100 genome assembly
Supplementary files format and content: Raw_gene_counts

source_name: Cardiac

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: isoproterenol (5 mg/kg/d),10 days; canagliflozin (3 mg/kg/d),4 weeks/exercised (60min/d), 4weeks.

value: Cardiac

value: Sprague Dawley


title: Rat; isoproterenol (5 mg/kg/d),10 days; exercised (60min/d), 4weeks. [57]


title: Rat; isoproterenol (5 mg/kg/d),10 days; exercised (60min/d), 4weeks. [103]


title: Arabidopsis wild type 5 weeks growth replicate 4

city: Harpenden

first: Daniel

last: Smith

state: Hertfordshire

address: West Common

department: IDE

country: United Kingdom

institute: Rothamsted Research

description:
D35WR4
2823_WT_5week_4

data_processing:
Quality control: FastQC
Trimming: Trimmomatic
Mapping: HiSat2
Gene counts: R BioConductor SubRead package (Feature Counts)
Normalisation & DE calling: DESeq2
Assembly: Arabidopsis thaliana TAIR10.1
Supplementary files format and content: CSV, SubRead FeatureCounts

organism: Arabidopsis thaliana

source_name: hypocotyl

growth_protocol: Grown in Grobanks cabinets in Levington F2 + Sand compost in long day conditions (16h/8h) under 250 µmol m-2 sec-1 intensity light

extract_protocol:
RNA extraction from hypocotyls for RNA sequencing was performed with the RNeasy Mini Kit (QIAGEN) and treated with DNase Turbo DNA-free kit (Thermo Fisher Scientific). 50 to 60 hypocotyls were pooled per biological replicate. RNA quality was assessed on a 2100 Bioanalyzer (Agilent Technologies)
polyA isolation with TruSeq directional library preparation

value: hypocotyl

tag: ecotype

value: wild type hypocotyl

value: wild type

tag: time

value: 5 weeks


title: Rat; isoproterenol (5 mg/kg/d),10 days; canagliflozin (3 mg/kg/d),4 weeks. [133]


title: MUX6680

value: HN237 Pri

value: Primary


title: IVH1


title: WT1_S1_L_scRNA-seq

tag: age


title: Arabidopsis wild type 5 weeks growth replicate 3

description:
D35WR3
2823_WT_5week_3

tag: cell type


title: Arabidopsis wild type 5 weeks growth replicate 2

description:
D35WR2
2823_WT_5week_2


title: Rat; isoproterenol (5 mg/kg/d),10 days; canagliflozin (3 mg/kg/d),4 weeks. [143]

tag: treatment


title: IVHControl4

value: Untreated


title: Rat; isoproterenol (5 mg/kg/d),10 days; canagliflozin (3 mg/kg/d),4 weeks. [78]


title: Rat; isoproterenol (5 mg/kg/d),10 days [119]

value: isoproterenol (5 mg/kg/d),10 days


title: Arabidopsis wild type 5 weeks growth replicate 1

description:
D35WR1
2823_WT_5week_1


title: IVHControl2


title: Arabidopsis wild type 21 days growth replicate 4

description:
D21WR4
2823_WT_21day_4

value: 21 days


title: Rat; isoproterenol (5 mg/kg/d),10 days [79]


title: Rat; isoproterenol (5 mg/kg/d),10 days [98]


title: IVH4


title: IVH3


title: IVHControl1


title: Arabidopsis wild type 21 days growth replicate 2

description:
D21WR2
2823_WT_21day_2


title: Rat,Control [95]

value: Control


title: Rat,Control [115]


title: wt.f3.bsseq

city: Norwich

first: David

middle: B.

last: Lyons

state: Norfolk

address: Colney Lane

department: Cell and Developmental Biology

institute: John Innes Centre

data_processing:
Bisulfite libraries were mapped to the genome following adaptor trimming with trim_galore (https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md) using BSMAP (Xi and Li 2009) using default settings for all analyses, except single-read analyses, for which we used Bismark (Kruger and Andrews 2011).
BSMAP output was converted to per-base methylation scores with BSMAP's methratio.py script using the -r setting to remove PCR duplicates.
Methratio.py output was converted to GFF and further processed and analysed using commands and workflows outlined in https://github.com/dblyons/modeling_h1ddm1/
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-seperated methratio.py output: chromosome, position, strand, cytosine context, ratio eff_CT_count, C_count, CT_count, rev_G_count, rev_GA_count, CI_lower, CI_upper.

source_name: rosette leaf

growth_protocol: Arabidopsis were sown to soil, stratified for 4 days at 4degC and transferred to controlled environment chambers where they were grown in 16h light / 8hr dark at 20deg C.

extract_protocol:
DNA was isolated by pulverizing ~0.5 g of flash frozen rosette leaves of 4 week post-germination plants.  ~100 mg of resulting powder was used to extract genomic DNA (gDNA) with the DNeasy plant mini kit (Qiagen cat. no. 69104) per manufacturer's instructions. gDNA was subsequently sonicated with the Bioruptor Pico (Diagenode) to ~250 bp median fragment length using 10 cycles of 30 seconds on and off.  Agencourt Ampure beads (referred to as “beads” henceforth, cat. no. A63881) were then used at 2X volume to purify the sheared DNA.
Following ligation of methylated Truseq sequencing adapters (Illumina) to sheared DNA, bisulfite conversion of DNA was carried out according to manufacturer’s protocol (Qiagen Epitect Kit, cat. no. 59104) except without using carrier RNA.  DNA was purified twice with 1.2X beads and converted a second time to ensure complete bisulfite conversion of unmethylated cytosine. Libraries were constructed using NEBnext kits (NEB cat. no. E7645) or Nugen/Tecan Ovation Ultralow (cat. no. 0344NB-08) following the manufacturer's instructions.   NEB next indexing primers (cat. no. E7335S) were used for generating multiplexed libraries during PCR amplification of libraries.

value: rosette leaf


title: Anti-PD1, NOG-EXL, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Seurat version 3.1.5 for downstream analysis
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PDX

extract_protocol:
Tumors were removed, processed into single cell suspension using a GentleMACS dissociator (Miltenyi Biotec) as described in the manufacturer protocol. Single cell was captured, lysed and reverse transcribed into cDNA using the 10x Chromium Single Cell V(D)J Reagent Kits and 10x Chromium controller, as described in the manufacturer protocol.
Libraries were prepared for sequencing using 10x Chromium Single Cell V(D)J Reagent Kits

value: PDX

tag: cell line

value: patient-derived primary cancer culture

value: cancer cell and CD8 T cells

value: NOG-EXL (hGM-CSF/hIL-3 NOG)


title: Arabidopsis wild type 21 days growth replicate 1

description:
D21WR1
2823_WT_21day_1


title: Control, NOG-EXL, scRNAseq

description: 10x Genomics


title: Arabidopsis wild type 15 days growth replicate 3

description:
D15WR3
2823_WT_15day_3

value: 15 days


title: h1ddm1.f3_3.bsseq


title: h1ddm1drm2.f7_2.bsseq


title: Arabidopsis wild type 15 days growth replicate 2

description:
D15WR2
2823_WT_15day_2


title: h1ddm1drm2.f6_2.bsseq


title: CT-vIII, 5898-D2C7-IT + αCD40, Day 3, Replicate 2

city: Durham

first: Vidyalakshmi

last: Chandramohan

state: NC

address: 181c MSRB1, 203 Research Drive

department: Neurosurgery

institute: Duke University

description:
5888, 5898, 5881 raw_counts.csv
The additional three samples, 5890, 5877, 5882, are the replicates of the Day 3 control sample that was used for comparison with the Day 3 D2C7-IT + αCD40 treatment samples 5888, 5898, 5881. Since the processed data for the Day 3 control group was already included in the “5890, 5877, 5882, 5878, 5891, 5896 raw_counts.csv” file, this information was not highlighted in the "5888, 5898, 5881 raw_counts.csv" file.

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Following QC, raw data sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus (GRCm38) reference genome available on ENSEMBL using the STAR aligner v.2.5.2b to generate BAM files. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38
Supplementary files format and content: raw counts

source_name: Brain tumor

growth_protocol: Each mouse underwent intracranial tumor implantations with 2x10^5 CT-VIII cells on day 0, in the right hemisphere, at 0.5 mm anterior and 2.0 mm lateral to bregma, and at a depth of 3.3 mm below the skull.

extract_protocol:
RNA extraction, library preparations, and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA) as follows: Total RNA was extracted from flash-frozen brain tumor tissue samples collected post-therapy and 3 days post-therapy (N=3/group/time point) using Qiagen RNeasy Plus Universal mini kit following the manufacturer’s instructions (Qiagen).
mRNAs were first enriched with Oligo(dT) beads and RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB).

treatment_protocol: On day 6 post-tumor implantation, mice were treated with D2C7 (0.2 μg) and αCD40 (10-300 μg; Clone FGK4.5/FGK45 Bio-X-Cell) mono or combination therapies by convection-enhanced delivery using Alzet Micro-Osmotic Pumps (Model 1007D) (Durect Corporation) at a rate of 0.5 µl/hr for 72 hr. Control groups were treated with 2% MSA-PBS with 100 μg rat IgG2a Ab (Bio-X-Cell InVivoPlus Clone 2A3). On day 9 at the end of 72 hr CED, the Alzet Micro-Osmotic Pumps were removed, and tumors (n=3) were harvested for each treatment group immediately or 3 days post-tretament.

value: Brain tumor

value: CT-2A-dmEGFRvIII-Firefly Luciferase

value: Glioma cell line

value: mouse EGFR variant III and firefly luciferase transduced

value: D2C7-IT + αCD40, Day 3


title: h1ddm1drm2.f7_1.bsseq


title: CT-vIII, 5881-D2C7-IT + αCD40, Day 3, Replicate 3


title: IVHControl3


title: Arabidopsis mutant 5 weeks growth replicate 4

description:
D35DR4
2823_Mut_5week_4

value: hypocotyl

value: mutant hypocotyl

value: dwarf (CRK10 (At4g23180) mutant)

value: 5 weeks


title: CT-vIII, 5888-D2C7-IT + αCD40, Day 3, Replicate 1


title: h1ddm1drm2.f5_2.bsseq


title: Arabidopsis mutant 5 weeks growth replicate 3

description:
D35DR3
2823_Mut_5week_3


title: Arabidopsis wild type 21 days growth replicate 3

description:
D21WR3
2823_WT_21day_3

value: wild type hypocotyl

value: wild type

value: 21 days


title: CT-vIII, 5884-D2C7-IT, Day 3, Replicate 3

description:
5893, 5897, 5884 raw_counts.csv
The additional three samples, 5890, 5877, 5882, are the replicates of the Day 3 control sample that was used for comparison with the Day 3 D2C7-IT treatment samples 5893, 5897, 5884. Since the processed data for the Day 3 control group was already included in the “5890, 5877, 5882, 5878, 5891, 5896 raw_counts.csv” file, this information was not highlighted in the "5893, 5897, 5884 raw_counts.csv" file.

value: D2C7-IT, Day 3


title: h1ddm1drm2.f6_1.bsseq

value: rosette leaf


title: CT-vIII, 5897-D2C7-IT, Day 3, Replicate 2


title: Arabidopsis mutant 5 weeks growth replicate 2

description:
D35DR2
2823_Mut_5week_2


title: h1ddm1drm2.f2_1.bsseq


title: h1ddm1.f11.bsseq


title: CT-vIII, 5893-D2C7-IT, Day 3, Replicate 1


title: h1ddm1drm2.f3_1.bsseq


title: Arabidopsis wild type 15 days growth replicate 4

description:
D15WR4
2823_WT_15day_4


title: CT-vIII, 5896-αCD40, Day 3, Replicate 3

description: 5890, 5877, 5882, 5878, 5891, 5896 raw_counts.csv

value: αCD40, Day 3


title: h1ddm1cmt3.f7_2.bsseq


title: CT-vIII, 5878-αCD40, Day 3, Replicate 1


title: Arabidopsis mutant 21 days growth replicate 3

description:
D21DR3
2823_Mut_21day_3


title: CT-vIII, 5891-αCD40, Day 3, Replicate 2


title: h1ddm1cmt3.f7_1.bsseq


title: Arabidopsis mutant 21 days growth replicate 4

description:
D21DR4
2823_Mut_21day_4


title: Arabidopsis mutant 21 days growth replicate 2

description:
D21DR2
2823_Mut_21day_2


title: Arabidopsis wild type 15 days growth replicate 1

description:
D15WR1
2823_WT_15day_1


title: h1ddm1cmt3.f5_2.bsseq


title: CT-vIII, 5877-Vehicle, Day 3, Replicate 2

value: Vehicle Control, Day 3


title: Arabidopsis mutant 15 days growth replicate 4

description:
D15DR4
2823_Mut_15day_4

value: 15 days


title: CT-vIII, 5882-Vehicle, Day 3, Replicate 3

value: Brain tumor


title: Arabidopsis mutant 21 days growth replicate 1

description:
D21DR1
2823_Mut_21day_1


title: CT-vIII, 5890-Vehicle, Day 3, Replicate 1

value: CT-2A-dmEGFRvIII-Firefly Luciferase


title: h1ddm1cmt3.f6_2.bsseq


title: Arabidopsis mutant 5 weeks growth replicate 1

description:
D35DR1
2823_Mut_5week_1


title: h1ddm1cmt3.f6_1.bsseq


title: CT-vIII, 5889-D2C7-IT + αCD40, Day 0, Replicate 2

description:
5887, 5889, 5880 raw_counts.csv
The additional three samples, 5886, 5894, 5895, are the replicates of the Day 0 control sample that was used for comparison with the Day 0 D2C7-IT + αCD40 treatment samples 5887, 5889, 5880. Since the processed data for the Day 0 control group was already included in the “5886, 5894, 5895, 5879, 5900, 5885 raw_counts.csv” file, this information was not highlighted in the "5887, 5889, 5880 raw_counts.csv" file.

value: Glioma cell line

value: D2C7-IT + αCD40, Day 0


title: h1ddm1cmt3.f4_1.bsseq


title: CT-vIII, 5880-D2C7-IT + αCD40, Day 0, Replicate 3

value: mouse EGFR variant III and firefly luciferase transduced


title: Arabidopsis mutant 15 days growth replicate 3

description:
D15DR3
2823_Mut_15day_3

value: hypocotyl


title: Arabidopsis mutant 15 days growth replicate 1

description:
D15DR1
2823_Mut_15day_1

value: mutant hypocotyl


title: Arabidopsis mutant 15 days growth replicate 2

description:
D15DR2
2823_Mut_15day_2

value: dwarf (CRK10 (At4g23180) mutant)


title: h1ddm1cmt2.f7_2.bsseq


title: CT-vIII, 5899-D2C7-IT, Day 0, Replicate 3

description:
5876, 5892, 5899 raw_counts.csv
The additional three samples, 5886, 5894, 5895, are the replicates of the Day 0 control sample that was used for comparison with the Day 0 D2C7-IT treatment samples 5876, 5892, 5899. Since the processed data for the Day 0 control group was already included in the “5886, 5894, 5895, 5879, 5900, 5885 raw_counts.csv” file, this information was not highlighted in the "5876, 5892, 5899 raw_counts.csv" file.

value: D2C7-IT, Day 0


title: h1ddm1cmt3.f5_1.bsseq


title: wt_1_f3.rna

extract_protocol:
Rosette leaves from the F3 generation were flash frozen in liquid nitrogen, pulverized with mortar and pestle on dry ice, and the resulting material was subjected to vortexing in Trizol (Invitrogen, cat. no. 15596-026).  Chloroform was then added at one-fifth the total volume and further vortexing was carried out until the solution appeared homogenous.  RNA was subsequently pelleted in ice-cold isopropanol. The resuspended RNA was subjected to rRNA removal with Ribo-zero plant kit (Illumina, MRZPL1224) according to the manufacturer’s protocol.
50ng ribo-depleted was used for library preparation with the Scriptseq kit (Epicentre, cat. no. SSV21124) following the manufacturer’s protocol but with the following modifications: the RNA fragmentation step was extended to 10 minutes, and the temperature was increased to 90°C.


title: h1ddm1cmt3.f3_1.bsseq


title: wt_2_f3.rna


title: h1ddm1cmt2.f7_1.bsseq


title: h1ddm1cmt2.f6_2.bsseq


title: h1ddm1_3_f3.rna


title: h1ddm1cmt2.f6_1.bsseq


title: CT-vIII, 5892-D2C7-IT, Day 0, Replicate 2


title: CT-vIII, 5876-D2C7-IT, Day 0, Replicate 1


title: h1ddm1_1_f3.rna


title: CT-vIII, 5885-αCD40, Day 0, Replicate 3

description: 5886, 5894, 5895, 5879, 5900, 5885 raw_counts.csv

value: αCD40, Day 0


title: h1ddm1_2_f3.rna


title: CT-vIII, 5900-αCD40, Day 0, Replicate 2


title: h1_3_f3.rna


title: CT-vIII, 5879-αCD40, Day 0, Replicate 1


title: h1_2_f3.rna


title: TRAF5

city: Houston

first: Huan

last: Meng

state: Texas

address: One Baylor Plaza BCM 130

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

data_processing:
The Fastq files containing raw RNA-Seq reads were aligned to the human genome (GRCh38/hg38) using HISAT2 (2.1.0). The paired-end reads below MAPQ quality score 15 were removed. The RNA-Seq quantification was performed with featureCounts (1.6.4, default parameters). Protein-coding genes were quantified by UCSC RefSeq gene annotation.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: TRAF4-overexpressing LNCaP cells

growth_protocol: TRAF4 overexpressing or control LNCaP cells were grown in   DMEM-Ham’s F-12 with 10% fetal bovine serum, 5 mg/ml insulin, 13.65 pg/ml triiodothyronine,   5 mg/ml apo-transferrin, 0.244 mg/ml d-biotin, and 25 mg/ml adenine.

extract_protocol:
The RNA samples from LNCaP control or TRAF4 overexpressing cells (n=5) were isolated with the miRNeasy Mini Kit (Qiagen) per the manufacturer’s instructions. The quantity and integrity of the RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and 1% agarose gel electrophoresis.
500ng to 1ug of total RNA from the individual cell lines or tumor tissues were converted into mRNA-Seq libraries with the non-directional, Poly-A tail selection and library preparation kit (Illumina) per the manufacturer’s protocol. Only the RNA samples with RIN values ≥8 were used for constructing the cDNA libraries. The cDNA libraries were sequenced using the Illumina Platform PE150 Q30≥80% with a paired-end read length of 150 bp for an average of 30 million paired-end reads per sample.

treatment_protocol: Cells were transfected with plasmid DNA using Lipofectamine 3000 and siRNA using Lipofectamine RNAiMAX transfection reagent (both from Thermo Fisher Scientific) following the manufacturer’s protocol. Virus packaging was performed in HEK293T cells after cotransfection of plasmid with the packaging plasmid psPAX2 and envelope plasmid pMD2.G using Lipofectamine 3000. Viruses were harvested 48 hours after transfection, and viral titers were determined. Target cells were infected with recombinant lentivirus-transducing units in the presence of 8 μg/ml Polybrene (Sigma-Aldrich).

tag: gender

value: Male

value: LNCaP

value: 50 years adult

value: TRAF4-overexpressing LNCaP cells


title: TRAF4


title: CT-vIII, 5887-D2C7-IT + αCD40, Day 0, Replicate 1


title: h1_1_f3.rna

value: rosette leaf


title: TRAF3


title: CT-vIII, 5895-Vehicle, Day 0, Replicate 3

value: Vehicle Control, Day 0


title: TRAF1


title: CT-vIII, 5894-Vehicle, Day 0, Replicate 2


title: ddm1_3_f3.rna


title: TRAF2


title: CT-vIII, 5886-Vehicle, Day 0, Replicate 1


title: Lenti4

source_name: Control LNCaP cells

value: Control LNCaP cells


title: Lenti5


title: ddm1_1_f3.rna


title: wt.sp.f5.bsseq

source_name: sperm

extract_protocol:
Open flowers of F4 or F5 plants (which is here denoted as F4 or F5 sperm, respectively) werecollected for pollen isolation in Galbraith buffer (45 mM MgCl2, 30 mM sodium citrate, 20 mMMOPS, 1% Triton-X-100, pH7.0) by vortexing at 2000 rpm for 3 min. Flower parts wereremoved by straining through a 40 micron filter. Pollen grains were obtained by centrifugation at2600 g for 5 minutes and broken down with glass beads (Sigma). The lysate was then transferredto a 40 micron cell strainer and the flow-through was centrifuged at 800 g for 10 min at 4°C. Thepellet was re-suspended in Galbraith buffer and stained with SYBR Green for fluorescence-activated cell sorting (FACS). Vegetative nuclei and sperm nuclei (SN) were separated andcollected based on size and fluorescence intensity. DNA was extracted from SN withChargeSwitch gDNA Micro Tissue Kit (ThermoFisher cat. no. CS11203) following manufacturer’s instructions. Briefly, SN were lysed in lysis buffer with proteinase K provided bythe kit in a 55°C water bath overnight. RNA was digested with RNase A at room temperature for30 minutes, then DNA was captured with magnetic beads provided, washed, and eluted.
After quantification by fluorometry, about 10-20 ng of DNA was used for bisulfite-sequencing librarypreparation with Ovation Ultralow Methyl-Seq DR Multiplex System (Nugen part no. 0336)following manufacturer’s instructions. Briefly, DNA was sonicated with Bioruptor sonicator, endrepaired, ligated to adapters which contain indexes, and bisulfite converted twice with EpiTectFast DNA Bisulfite Kit (Qiagen 59802) following manufacturer’s instructions. After PCRamplification, libraries were purified with Agencourt RNAClean XP Beads.

value: sperm


title: Mouse GBM tumor tissue 2

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

data_processing:
Reads were aligned with CellRanger (10x Genomics, version 6.1.2) against customized mouse reference library (mm10) to produce sparse numerical matrices for each sample, with gene-level counts of unique molecular identifiers (UMI) identified for all single cells passing default quality control metrics.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Mouse Tumor (GBM)

extract_protocol:
Cdh5-CreERT2;Rosa-LSL-tdTomato mice bearing RCAS-induced tumors were euthanized and perfused with PBS supplemented with EDTA. GBM tumors and brain tissue from a healthy mouse were harvested and digested with collagenase-II and DNase. Single cell suspension was prepared after filtering using a mesh strainer with 100-μm pores.
Cell samples were prepared and analyzed following a manufacturer’s V3 library protocol (10x Genomics) and single-cell RNA-seq at the next-generation sequencing core at the University of Pennsylvania.
scRNA-Seq

treatment_protocol: GBM was induced by orthotopic injection in Cdh5-CreERT2;Rosa-LSL-tdTomato mice (6-8 weeks old).

tag: disease state

value: glioblastoma (GBM)

value: GBM tumor


title: Mouse GBM tumor tissue 3


title: wt.sp.f4.bsseq


title: Mouse GBM tumor tissue 1


title: Mouse normal brain tissue

source_name: Mouse Brain

value: normal

value: brain


title: Lenti1


title: h1.sp.f5.bsseq


title: Kidney_Fh1+/+_WT_day5_rep5

city: London

first: Shamith

last: Samarajiwa

address: ICTEM Building, Hammersmith Campus, Du Cane Road,

department: Genetics and Genomics Section  Department of Metabolism, Digestion and Reproduction

institute: Imperial College London

data_processing:
Sequenced reads with a quality score of >20 were trimmed, and adaptor sequencers were removed with cutadapt v1.1,0 then mapped to mm10 (GRCm38) whole genome using STAR aligner v2.6.0c with GENCODE GRCm38 vM17 gtf annotation
read count was done with Rsubread and differential expression computed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Kidney

extract_protocol:
Kidneys were removed, flash frozen in liquid nitrogen, the tissue was homogenized using the PreCellys system and RNA was harvested using Qiagen kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Recombination was induced in animals by intra-peritoneal injection of 3 x 2mg tamoxifen in corn oil (injections every other day). Kidneys were collected at days 5 and 10 post-induction.

value: mixed C57BL/6 129/SvJ

value: wild-type Fh1+/+

value: Kidney

tag: timepoint

value: day 5 post induction

value: 3 x 2mg IP tamoxifen


title: h1ddm1.sp.f5.bsseq


title: Kidney_Fh1+/+_WT_day5_rep4


title: Kidney_Fh1+/+_WT_day5_rep3


title: ddm1.sp.f5.bsseq


title: Kidney_Fh1+/+_WT_day5_rep2


title: ddm1.sp.f4.bsseq


title: h1ddm1.sp.f4.bsseq


title: Kidney_Fh1+/+_WT_day5_rep1


title: ddm1_2_f3.rna


title: h1ddm1.f9_2.bsseq


title: Kidney_Fh1+/+_WT_day10_rep5

value: day 10 post induction


title: MYSM1_ribosome_profiling_rep3

city: Boston

first: Jiawei

last: Zhao

state: Massachusetts

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
sequence were aligned to rRNA index to remove rRNA reads
non-rRNA reads were trimmed for adaptor sequences and sequences with too short reads
trimmed sequences were aligned by STAR aligner
aligned reads were run by riboCode software for ORF identification
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw read counts of ORFs for each sample
Library strategy: Ribo-seq

source_name: CD34+CD45RA-CD90+ cells, MYSM1 edited, day 5 post-nucleofection

growth_protocol: Immobilized bone marrow CD34+ cells were cultured in CD34+ cell expansion medium with Stemcell Technology's serum free expansion medium as base medium supplemented with 1X cc100 supplement, 100ng/ml TPO and 35nM UM171

extract_protocol:
cells were lysed in ribosome profiling buffer (see publication for recipe and details)
extracted RNAs were sedimented for ribosome protected fragment by ultracentrifugation over 1M sucrose cushion. 26-33nt RNA fragments were excised for library preparation

treatment_protocol:
CD34+ cells were nuclefected by AAVS1 or MYSM1 CRISPR RNPs
all cells were treated 5min before profiling and maintained in 100ug/ml cycloheximide for the entire protocol

tag: cell markers

value: HSPC

value: MYSM1 KO

value: Day 5


title: MYSM1_ribosome_profiling_rep1


title: MYSM1_ribosome_profiling_rep2


title: Lenti3

value: Male

value: LNCaP

value: 50 years adult


title: h1ddm1.f9_1.bsseq

tag: tissue

value: rosette leaf


title: greenCUTRUN_E93_72-Pupa_bioRep-2

first: Nicolas

last: Gompel

address: Grosshaderner Str. 2

data_processing:
library strategy: greenCUT&RUN
Libraries were demultiplexed and trimmed, and then aligned to the reference genome UCSC dm6 using Bowtie2 with following parameters: --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
The aligned reads were filtered and cleaned as previously described in ATAC-seq(GSE142176).
BigWig files were converted from normalized bedGraph files generated by MACS2 with following settings: -f BAMPE --keep-dup all -q 0.01 -g 1.2e+8 -B --SPMR.
Assembly: dm6
Supplementary files format and content: BigWig files for normalized signal track

organism: Drosophila melanogaster

source_name: Pupal wings

growth_protocol: D. melanogaster protein trap line E93GFSTF (Bloomington #43675) was maintained on standard cornmeal medium at 25ºC with a 12:12 day-night light cycle.

extract_protocol:
70-90 wings per biological replicate at 72% pupal development from D. melanogaster protein trap line E93GFSTF were transferred into a 5 ml Eppendorf tube with cold 1x PBS and 6 mM MgCl2, rocked at 4°C with 1x cold lysis buffer for 5 min and then crosslinked (4 min) with the crosslink buffer. After crosslink, the wings were immediately quenched with glycine, and then transferred into a glass well with 50 μl cold XL WB buffer and cut coarsely (3 pieces per wing). Homogenization was performed with a 2 ml Dounce using pestle A for 12 strokes and then pestle B for 30 strokes. The homogenate was incubated on ice for 30 min, and then centrifuged at 1000 g for 10 min at 4°C with an addition of 500 μl of XL WB. The nuclei pellet was resuspended with 100 μl XL WB and processed for greenCUT&RUN. The greenCUT&RUN was performed following the protocol from Koidl et al. (doi: 10.1002/cpz1.266) until the DNA isolation step. The concentration of digitonin in the digitonin buffer was 0.05%. Reverse crosslink and DNA isolation were done as described in this project in the section of CUT&RUN against H3K27ac.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 2) following a protocol published on protocols.io (DOI: dx.doi.org/10.17504/protocols.io.wvgfe3w).

value: Pupal wings

value: 72% of pupal development

tag: Sex


title: Kidney_Fh1+/+_WT_day10_rep4

tag: strain


title: Lenti2

tag: genotype

value: Control LNCaP cells


title: greenCUTRUN_E93_72-Pupa_bioRep-1

tag: developmental stage


title: AAVS1_ribosome_profiling_rep3

source_name: CD34+CD45RA-CD90+ cells, AAVS1 edited, day 5 post-nucleofection


title: h1ddm1.f8_2.bsseq


title: CD34+CD45RA-CD90+ scRNAseq, edited by MYSM1, day 4 post-nucleofection

data_processing:
Cellranger
Sequence reads were analyzed by 10Xgenomics software Cellranger with default setting
matrix file was used for downstream differential gene expression analysis by Seurat package in R
Assembly: hg38
Supplementary files format and content: matrix files, barcode files, feature files

source_name: HSPC

extract_protocol:
CD34+CD45RA-CD90+ cells were FACS sorted and 7000 cells were used in 10Xgenomics single cell RNA seq library preparation kit following manufacturer's protocols exactly
library constructed using 10Xgenomics single cell RNA seq library construction kit following manufacturer's instruction

treatment_protocol: CD34+ cells were nuclefected by AAVS1 or MYSM1 CRISPR RNPs

value: CD34+CD45RA-CD90+ cells

value: Day 4


title: CD34+CD45RA-CD90+ scRNAseq, edited by AAVS1, day 3 post-nucleofection


title: Kidney_Fh1+/+_WT_day10_rep3

value: mixed C57BL/6 129/SvJ

value: wild-type Fh1+/+


title: CUTRUN_H3K27ac_67-Pupa_bioRep-2

data_processing:
library strategy: CUT&RUN
Libraries were demultiplexed and trimmed, and then aligned to the reference genome UCSC dm6 using Bowtie2 with following parameters: --end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
The aligned reads were filtered and cleaned as previously described (GSE142176).
Peak calling was performed by MACS2 with following settings: -f BAMPE --keep-dup all -q 0.01 -g 1.2e+8 -B --SPMR.
BigWig files were converted from normalized bedGraph files generated by MACS2 above.
Assembly: dm6
Supplementary files format and content: BigWig files for normalized signal track,narrowpeak files for peaks called by MACS2.

growth_protocol: D. melanogaster line D2, a transgenic line used in previous study (GSE142176), was maintained on standard cornmeal medium at 25ºC with a 12:12 day-night light cycle.

extract_protocol:
35-45 wings per biological replicate at 67% pupal development from D. melanogaster line D2 were transferred into a 5 ml Eppendorf tube with cold 1x PBS and 6 mM MgCl2, rocked at 4°C with 1x cold lysis buffer for 5 min and then lightly crosslinked (1 min) with the crosslink buffer. After light crosslink, the wings were immediately quenched with glycine, and then transferred into a glass well with 50 μl cold XL WB buffer and cut coarsely (3 pieces per wing). Homogenization was performed with a 2 ml Dounce using pestle A for 12 strokes and then pestle B for 30 strokes. The homogenate was incubated on ice for 40-50 min, and then centrifuged at 1000 g for 10 min at 4°C with an addition of 500 μl of XL WB. The nuclei pellet was resuspended with 100 μl XL WB and processed for CUT&RUN. The CUT&RUN steps were performed following the instructions from EpiCypher, including bead activation, binding cells to activated beads, binding of antibodies, binding of pAG-MNase, targeted chromatin digestion and release, and reverse crosslinking. 1 μl of antibody against H3K27ac (Active Motif #39034) was used. DNA was then purified with Qiagen MinElute kit and subsequently processed for library preparation.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 2) following a protocol published on protocols.io (DOI: dx.doi.org/10.17504/protocols.io.wvgfe3w).

value: 67% of pupal development


title: h1ddm1.f7_2.bsseq


title: AAVS1_ribosome_profiling_rep2


title: Kidney_Fh1+/+_WT_day10_rep2

value: Kidney

value: 3 x 2mg IP tamoxifen


title: CUTRUN_H3K27ac_67-Pupa_bioRep-1


title: Kidney_Fh1+/+_WT_day10_rep1

value: day 10 post induction


title: h1ddm1.f7_1.bsseq


title: Dmel_78-Pupa_bioRep-2

data_processing:
ATAC-seq libraries were processed as described (GSE142176; doi: 10.1073/pnas.2004003117):  The sequenced libraries were demultiplexed, trimmed, and aligned to the reference genome UCSC dm6 using Bowtie2 with following settings: -X 2000; --fr; --very-sensitive.
The aligned reads were then filtered by Picard with the following steps: clean sam, FixMate information, MarkDuplicate. The PCR duplicates were subsequently removed by SAMtools.
BigWig files were converted from normalized bedGraph files, which were generated by MACS2 with following settings: --keep-dup all; -q 0.01; --nomodel; --shift -100; --extsize 200.
Peaking calling was performed using HOMER with following settings: -style histone -size 100 -minDist 100 -gsize 1.2e+8 -o auto.
Assembly: dm6 for D. melanogaster; GCF_000233415.1 for D. biarmipes
Supplementary files format and content: BigWig files for normalized signal track, bed files for peaks called by HOMER.

extract_protocol:
Nuclei were extracted and prepared as described before (GSE142176) with some modifications: dissected wings were immediately moved into cold 1x lysis buffer after rinsing. 24 0% pupal development wing discs, 14-17 wings from at least 11 individuals at 47% pupal development, and 24 wings from later stages were used for following steps, respectively. Only the pupal wings older than 60% of pupal development were cut before disruption. Samples were incubated on ice for 20-30 min before and after disruption. For tagmentation: the reaction was set up with 18 µl of Tagment DNA Buffer (Illumina #15027866) with nuclei, plus 2 µl of Tagment DNA Enzyme (Illumina #15027865).
ATAC-seq libraries were prepared as described before (GSE142176; doi: 10.1073/pnas.2004003117).  The libraries were amplified by NEBNext High-Fidelity 2X PCR Master Mix (NEB Cat. M0541S) for 9-11 PCR cycles, purified by Agencourt AMPure XP beads (Beckman Coulter) with double size selection (0.5x and 2.0x), and validated by Bioanalyzer using High Sensitive DNA chip (Agilent).

value: 78% of pupal development


title: h1ddm1.f6_2.bsseq


title: YAP-/- 2_EB_d5 (RNA-seq)

data_processing:
Quality Control: FastQC
Trimming adaptor and low quality seqs: Trimmomatic
Alignment: Star-aligner
Read counting: FeatureCount
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: EB

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA Plus Kit (Macherey-Nagel, Düren, Germany).
Library preparation was carried out using QuantSeq 3´-mRNA (Lexgon) according to the manufacturer's instructions. Sequencing was done using NovaSeq 6000 sequencer (Ilumina). Library preparation and sequencing was carried out by Life&Brain (Bonn, Germany).

value: YAP-/-

value: EB

value: female

tag: differentiation timepoint

tag: sample group

value: Day 5 EB KO


title: Kidney_Fh1-/-_HOM_day5_rep5

value: null Fh1-/-

value: day 5 post induction


title: Dmel_69-Pupa_bioRep-2

value: Pupal wings

value: 69% of pupal development

value: Male


title: WT 3_ EB_d5 (RNA-seq)

value: WT

value: male

value: Day 5 EB


title: Dmel_60-Pupa_bioRep-2

value: 60% of pupal development


title: h1ddm1.f5_1.bsseq

tag: ecotype

value: rosette leaf


title: Kidney_Fh1-/-_HOM_day5_rep3

value: mixed C57BL/6 129/SvJ

value: Kidney

value: 3 x 2mg IP tamoxifen


title: Kidney_Fh1-/-_HOM_day5_rep4


title: Dmel_48-Pupa_bioRep-2

value: 48% of pupal development


title: h1ddm1.f4_2.bsseq


title: LPSControl1

source_name: choroid plexus (ChP)

extract_protocol:
Immediately following transcardial perfusion with ice cold TBS (pH = 7.60), the brain was isolated and placed in an ice-cold saline bath. Brains were cut sagittally along the interhemispheric line to expose the lateral ventricles, and choroid plexuses were rapidly but carefully dissected from both lateral ventricles using sharp forceps under magnification. Each brain yielded ~3 mg of choroid plexus tissue total, which was collected into a 1.5 mL tube, snap frozen in liquid nitrogen, and stored at -80oC until use.
Full length high quality total cell RNA isolated by Qiagen RNAeasy micro kit (Quigen, https://www.qiagen.com/us/shop/pcr/rneasy-micro-kit/). ChP cells were homogenized in 350ul RLT buffer with beta-mercaptoethanol in Tissuelyzer for 10 mins and proceed according to the instructions in RNAeasy Micro RNA kit and RNAs was eluted in 18ul dH2O. 16ul of elutant was recovered and 1.2ul was used for the QC. Libraries were run on an Illumina HiSeq 2500 at the Yale Center for Genome Analysis. The R/Bioconductor package “DESeq2” was used to identify differentially expressed genes between cell populations derived from control, IVH-treated and LPS-treated rats (Love et al., 2014). Genes with a log2-fold change expression greater than 3 and a q-value less than 0.01 were considered significant. The R ComplexHeatmap package was used to visualize the heatmap expression of highly variable genes (Gu et al., 2016). Volcano plots were generated using the R package EnhancedVolcano (Blighe et al., 2019).

value: Untreated


title: Kidney_Fh1-/-_HOM_day5_rep2


title: h1ddm1.f5_2.bsseq


title: h1ddm1.f3_2.bsseq


title: AAVS1_ribosome_profiling_rep1

value: HSPC

tag: time

value: Day 5


title: Kidney_Fh1-/-_HOM_day5_rep1

value: null Fh1-/-


title: iPSC YAP-/- 2_ECTO (RNA-seq)

description: iPSC 102 #30 ECTO

source_name: iPSC

value: YAP-/-

value: iPSC

value: female

value: ectoderm


title: Dmel_0-Pupa_bioRep-2

value: Pupal wings

value: 0% of pupal development

value: Male


title: Dmel_78-Pupa_bioRep-1

value: 78% of pupal development


title: iPSC YAP-/- 2_ENDO (RNA-seq)

description: iPSC 102 #30 ENDO

value: endoderm


title: h1ddm1.f3_1.bsseq

value: rosette leaf


title: Kidney_Fh1-/-_HOM_day10_rep5

value: mixed C57BL/6 129/SvJ

value: Kidney

value: day 10 post induction


title: Dmel_69-Pupa_bioRep-1

value: 69% of pupal development


title: YAP-/- 1_EB_d5 (RNA-seq)

value: EB

value: Day 5 EB KO


title: iPSC YAP-/- 2_MESO (RNA-seq)

description: iPSC 102 #30 MESO

value: mesoderm


title: h1ddm1.f2_2.bsseq


title: Kidney_Fh1-/-_HOM_day10_rep4

value: null Fh1-/-

value: 3 x 2mg IP tamoxifen


title: iPSC YAP-/- 2_ SC (RNA-seq)

description: iPSC 102 #30 undifferentiated

value: YAP-/-

value: iPSC

value: female

value: undifferentiated


title: h1ddm1.f2_1.bsseq


title: Dmel_60-Pupa_bioRep-1

value: Pupal wings

value: 60% of pupal development

value: Male


title: Kidney_Fh1-/-_HOM_day10_rep3


title: WT 1_ EB_d5 (RNA-seq)

value: WT

value: Day 5 EB


title: Kidney_Fh1-/-_HOM_day10_rep2

value: mixed C57BL/6 129/SvJ

value: Kidney


title: h1ddm1.f11_1.bsseq

value: rosette leaf


title: h1ddm1.f10_1.bsseq


title: Dmel_0-Pupa_bioRep-1

value: 0% of pupal development


title: iPSC YAP-/- 1_ECTO (RNA-seq)

description: iPSC 102 #20 ECTO

value: ectoderm


title: Kidney_Fh1-/-_HOM_day10_rep1

value: day 10 post induction


title: wt.f4.bsseq


title: Dmel_48-Pupa_bioRep-1

value: 48% of pupal development


title: iPSC YAP-/- 1_ENDO (RNA-seq)

description: iPSC 102 #20 ENDO

value: endoderm


title: h1.f4.bsseq


title: iPSC YAP-/- 1_SC (RNA-seq)

description: iPSC 102 #20 undifferentiated

value: YAP-/-


title: marmoset D6 PGCLCs, scRNAseq

city: Yiwu

first: keren

last: cheng

address: 1575 chouzhou bei road

institute: Zhejiang University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v.6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: calJac4
Supplementary files format and content: h5 files of raw counts tables
Supplementary files format and content: tar.gz files of velocity counts tables

source_name: Aggregate

extract_protocol:
To minimize the contamination with feeder cells, >30 colonies of cjiPSCs cultured on feeder layer were randomly picked under an inverted microscope. Aggregates were rinsed with PBS twice and dissociated into single cells with 0.1% trypsin/EDTA treatment for 15 min at 37°C with periodic pipetting. Cells were loaded into chromium microfluidic chips with the Chromium Next GEM Single Cell 3ʼReagent Kit (v3.1 chemistry) and then used to generate single-cell gel bead emulsions (GEMs) using the Chromium Controller (10× Genomics) according to the manufacturer’s protocol. GEM-RT was performed in a C1000 Touch Thermal Cycler with 96-Deep Well Reaction Module (Bio-Rad). All subsequent cDNA amplification and library construction steps were performed according to the manufacturer’s protocol. Libraries were sequenced using a 2 × 150 paired-end sequencing protocol on an Illumina HiSeq 4000 or NovaSeq 6000 instrument.
10X genomics

value: Aggregate

tag: age

value: Day 6

value: PGCLCs


title: marmoset D2 PGCLCs, scRNAseq

value: Day 2

tag: cell type


title: WT 2_ EB_d5 (RNA-seq)

value: EB

value: female


title: marmoset iPSC, scRNAseq

value: iPSC

value: Male