title: A. burtoni, testes, rep4 [smallRNA-seq]

data_processing:
The data resides within R1 so R2 was discarded. CutAdapt v1.15 (Martin, 2011) was used to remove adapters and reads shorter than 18 nucleotides with options -a TGGAATTCTCGGGTGCCAAGG   minimum-length 18 -o.
We selected small RNAs in the piRNA size range, between 24 and 35 nucleotides long, for further analysis. We have done this size selection using CutAdapt v1.15 (Martin, 2011) with options ‑‑minimum-length 24 --maximum-length 35.
We mapped the 24-35 nucleotide long reads to the genome using STAR v2.5.4b (Dobin et al., 2013), with options --outTmpDir --genomeDir   --readFilesIn --readFilesCommand zcat   outMultimapperOrder Random --outFilterMultimapNmax 100   outFilterMismatchNmax 2 --alignIntronMax 1 --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --winAnchorMultimapNmax 100 --alignEndsType EndToEnd   scoreDelOpen -10000 --scoreInsOpen -10000 --outSAMmultNmax 1   outFileNamePrefix. Reads from Lake Malawi cichlid species (A. calliptera, M. zebra, T. sp. "mauve") were all mapped to the A. calliptera genome fAstCal1.2. A. burtoni, P. nyererei, and O. niloticus reads were mapped to their genomes: AstBur1.0, PunNye1.0, and  O_niloticus_UMD_NMBU respectively. All these genomes are available at Ensembl.
To quantify piRNA counts mapping to TEs, we used featureCounts v1.6.0 (Liao et al., 2014) with options -a -o -t exon -M. The 24-35 nucleotide long BAM file was used as input. For Lake Malawi cichlids, featureCounts analysis was performed twice, using A. calliptera default and curated TE annotations. DESeq2 (Love et al., 2014) and custom scripts  were used to calculate normalized counts, generate plots and conduct statistical tests on an R framework (R Core Team, 2021).
Assembly: fAstCal1.2; AstBur1.0; PunNye1.0; O_niloticus_UMD_NMBU
Supplementary files format and content: Abur_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to  TEs in each A. burtoni sample.
Supplementary files format and content: Malawi_sRNA_NormTEcounts_CuratedAnnotation_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to TEs in each Lake Malawi cichlid sample. Using a curated TE annotation.
Supplementary files format and content: Malawi_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to TEs in each Lake Malawi cichlid sample.
Supplementary files format and content: Onil_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to  TEs in each O. niloticus sample.
Supplementary files format and content: Pnye_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to  TEs in each P. nyererei sample.

extract_protocol:
Tissue pieces were transferred to BeadBug tubes prefilled with 0.5 mm Zirconium beads (Merck, #Z763772) and 500-600 µl of TRIzol (Life Technologies, #15596026) was added to the tubes and mixed vigorously. Afterwards, we conducted the homogenisation using a BeadBug microtube homogeniser (Sigma, #Z764140) at approximately 4oC (in cold room). Each sample was homogenised with five BeadBug runs at maximum speed (4000 rpm) for 60 seconds each. Supernatant was then removed into a clean 1.5 mL tube. Centrifuged the lysates again, this time at maximum speed (approximately 21,000 G) for 5 minutes at 4oC. Transferred supernatant into a clean tube without disturbing the pellet and tissue debris. Mixed supernatant thoroughly 1:1 with 100% ethanol, pipetted the mix into a column provided in the Direct-zol RNA Miniprep Plus kit (Zymo Research, #R2072) and followed manufacturer’s instructions, using the recommended in-column DNase I treatment.
Samples were processed according to the NEXTFLEX® Small RNA-Seq Kit v4 with UDIs (PerkinElmer, #NOVA-5132-32) with a 1 µg starting input and 12 cycles of PCR. Samples were then pooled in equimolar amounts according to the TapeStation results and sequenced on a Novaseq 6000 system (PE50 on one lane of an SP Flowcell).


title: A. burtoni, ovary, rep2

status: Public on Apr 01 2024

type: SRA

city: Cambridge

first: Miguel

middle: Vasconcelos

last: Almeida

address: Tennis Court Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

description:
Abu_ov_rep2
rawCounts_mRNA_GenesAndTEs_Abur.txt
NormCounts_mRNA_TEs_Abur.txt

library_source: transcriptomic

data_processing:
Illumina adapters and reads with low-quality calls were filtered out with Trimmomatic v0.39 (Bolger et al., 2014) using options SLIDINGWINDOW:4:28 MINLEN:36.
We mapped trimmed reads to the genome, using STAR v2.5.4b (Dobin et al., 2013) with options --outTmpDir --readFilesCommand zcat ‑‑genomeDir ‑‑readFilesIn {R1} {R2} --outSAMtype BAM SortedByCoordinate ‑‑outFilterType BySJout --outFilterMultimapNmax 150 ‑‑winAnchorMultimapNmax 150 --alignSJoverhangMin 8 --alignSJDBoverhangMin 3 ‑‑outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 10000000 --alignMatesGapMax 100000000 --outFileNamePrefix. Reads from Lake Malawi cichlid species (A. calliptera, M. zebra, T. sp. "mauve") were all mapped to the A. calliptera genome fAstCal1.2. A. burtoni, P. nyererei, and O. niloticus reads were mapped to their genomes: AstBur1.0, PunNye1.0, and  O_niloticus_UMD_NMBU respectively. All these genomes are available at Ensembl.
The resulting BAM files were used as inputs for TEtranscripts v2.2.1 (Jin et al., 2015) with options -t -c --GTF --TE --stranded reverse ‑‑project --SortByPos.
For A. calliptera samples, gene expression (without TEs) was quantified from trimmed reads using salmon v1.5.1 (Patro et al., 2017), with options --seqBias --gcBias - validateMappings -l A -1 ‑2 -o -i.
DESeq2 (Love et al., 2014) and custom scripts were used to calculate log-normalized and TPM counts, generate plots and conduct statistical tests on an R framework (R Core Team, 2021).
Assembly: fAstCal1.2; AstBur1.0; PunNye1.0; O_niloticus_UMD_NMBU
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Acal.txt: Tab-delimited file includes raw counts for genes and TEs in each A. calliptera sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Acal.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each A. calliptera sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt: Tab-delimited file includes raw counts for genes and TEs in each Lake Malawi cichlid sample. Output of TEtranscripts, using a curated TE annotation.
Supplementary files format and content: NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each Lake Malawi cichlid sample. Using a curated TE annotation.
Supplementary files format and content: rawCounts_mRNA_Acal_brain_gonads.txt: Tab-delimited file includes raw counts in each A. calliptera sample. From Salmon output.
Supplementary files format and content: lengthScaledTPM_mRNA_Acal_brain_gonads.txt: Tab-delimited file includes length scaled TPM counts in each A. calliptera sample. From Salmon output.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Abur.txt: Tab-delimited file includes raw counts for genes and TEs in each A. burtoni sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Abur.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each A. burtoni sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Pnye.txt: Tab-delimited file includes raw counts for genes and TEs in each P. nyererei sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Pnye.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each P. nyererei sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Onil.txt: Tab-delimited file includes raw counts for genes and TEs in each O. niloticus sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Onil.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each O. niloticus sample.

molecule: total RNA

organism: Haplochromis burtoni

source_name: Ovary

extract_protocol:
Tissue pieces were transferred to BeadBug tubes prefilled with 0.5 mm Zirconium beads (Merck, #Z763772) and 500-600 µl of TRIzol (Life Technologies, #15596026) was added to the tubes and mixed vigorously. Afterwards, we conducted the homogenisation using a BeadBug microtube homogeniser (Sigma, #Z764140) at approximately 4oC (in cold room). Each sample was homogenised with five BeadBug runs at maximum speed (4000 rpm) for 60 seconds each. Supernatant was then removed into a clean 1.5 mL tube. Centrifuged the lysates again, this time at maximum speed (approximately 21,000 G) for 5 minutes at 4oC. Transferred supernatant into a clean tube without disturbing the pellet and tissue debris. Mixed supernatant thoroughly 1:1 with 100% ethanol, pipetted the mix into a column provided in the Direct-zol RNA Miniprep Plus kit (Zymo Research, #R2072) and followed manufacturer’s instructions, using the recommended in-column DNase I treatment.
Quality control, library preparation (directional, with poly-A enrichment), and mRNA sequencing (Illumina, PE150) was performed by Novogene. A. calliptera brain libraries and P.nyererei gonad libraries were prepared differently with the following protocol. We used 50-250 ng of total RNA for library production with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490), in conjunction with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, #E7760) and the NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB #E6440). Samples were then pooled in equimolar amounts and sequenced on a NovaSeq 6000 system (PE150 on one lane of an S1 Flowcell).

tag: tissue

value: Ovary

tag: genotype

value: wild-type


title: A. burtoni, testes, rep3 [smallRNA-seq]

source_name: Testes

value: Testes


title: PDACLungMetYFP _1

city: Boston

first: Lai Ping

last: Wong

state: MA

address: 185 Cambridge St

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

description:
CFa7-10
CFa7_YFP_GFP_CPM.txt

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using application at CLC genomic benchwork v 11.0.1 (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm9 using application at CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed at CLC genomic benchwork
Assembly: mm9

organism: Mus musculus

source_name: n/a YFP sorted cells

growth_protocol: YFP and GFP sorted tumor cells from orthotopic mouse models

extract_protocol:
RNA was harvested using RNAqueous-Micro Total RNA Isolation Kit (ThermoFisher Scientific). A minimum of 100ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Clontech's SMART-seq v4 Ultra Low Input RNA Kit followed by library preparation using Illumina's Nextera XT kit following manufacturer's protocols.

treatment_protocol:
n/a
n/a

tag: cell line

value: n/a YFP sorted cells

tag: cell type

value: PDAC Lung metastatic tumor cells

tag: time

value: 25.67 weeks


title: A. burtoni, testes, rep1 [smallRNA-seq]


title: A. burtoni, ovary, rep4 [smallRNA-seq]


title: SMC3au_M_P2_rep2

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

description:
150 bp x 150 bp
44_SMC3au_M_P3

library_source: genomic

data_processing:
library strategy: Capture-C
CapC-MAP was used for data processing, genomedigest was used to create a restriction site map for GRCg7b.
Target files for each oligo pool were generated with capClocation2fragment.
Reads were trimmed using cutadapt(v2.5) and mapped with bowtie(v1.2.2) CapC-MAP also uses samtools(v1.9) for processing and replicates were combined with combinereps.
Directionality analysis (min 3kb,max 250kb) used capturec-tools with captured_normalizedpileups as input and custom scripts used for plotting.
Assembly: GRCg7b
Supplementary files format and content: captured_normalizedpileup bedgraph files show piled-up intrachromosomal interaction counts for each target normalised to reads per million.

molecule: genomic DNA

organism: Gallus gallus

source_name: Bursa

growth_protocol: RPMI 10% FBS, 1% Chicken serum. Cells were culutured at 39C at 5% CO2.

extract_protocol:
Cells were lyse with SDS, washed, and triton X100 is used to sequester the SDS. Then genomic DNA was digedted with DpnII.
NEBNext Ultra II DNA library prep kit for Illumina protocol
NG-Capture-C. 3C library constructed above were double-hybridized with oligo pools to enrich the fragments coverirng Z or 5 centromere regions.

treatment_protocol: Cells were maintained at the concentration between 0.1-1 X10^6/ml. In order to block cells at G2, cells were treated with 2µM 1NMPP1 for 13 h. Prometaphase cells were collected at 30 min  except for SMC2-AID cells which was 45 min after washout of 1NMPP1. In order to deplete either SMC2 or SMC3, 125-150 µM auxin were added for the last 3h of 1NMPP1 treatment and then after until haresting cells. Nocodazole was added in release media at 0.5 µg/ml if required. Cells were crosslinked with 1% formaldehyde for 10 min, quenched with glycine, rinced with PBS. Cell pellets were frozen down with dryice.

value: Bursa

value: lymphoblast

value: female (ZW)

tag: treatment

value: Oligo pool 2


title: T. mauve, testes, rep4

description:
Tma_tes_rep4
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt

organism: Tropheops sp. 'mauve'


title: SMC3au_M_P3_rep1

description:
150 bp x 150 bp
42_SMC3au_M_P3

value: Oligo pool 3


title: SMC3au_M_P3_rep2

description:
150 bp x 150 bp
45_SMC3au_M_P3


title: SMC3au_M_P2_rep1

description:
150 bp x 150 bp
41_SMC3au_M_P3


title: SMC3au_M_P1_rep2

description:
150 bp x 150 bp
43_SMC3au_M_P1

value: Oligo pool 1


title: T. mauve, testes, rep3

description:
Tma_tes_rep3
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt


title: A. burtoni, testes, rep2

description:
Abu_tes_rep2
rawCounts_mRNA_GenesAndTEs_Abur.txt
NormCounts_mRNA_TEs_Abur.txt


title: SMC3au_G2_P3_rep2

description:
150 bp x 150 bp
39_SMC3au_G2_P3


title: SMC3au_G2_P1_rep2

description:
150 bp x 150 bp
37_SMC3au_G2_P1


title: SMC3au_G2_P2_rep2

description:
150 bp x 150 bp
38_SMC3au_G2_P2


title: T. mauve, testes, rep4 [smallRNA-seq]


title: SMC3au_M_P1_rep1

description:
150 bp x 150 bp
40_SMC3au_M_P1


title: T. mauve, testes, rep3 [smallRNA-seq]


title: T. mauve, testes, rep1 [smallRNA-seq]


title: SMC3au_G2_P1_rep1

description:
150 bp x 150 bp
34_SMC3au_G2_P1


title: M. zebra, testes, rep2

description:
Mze_tes_rep2
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt

organism: Maylandia zebra


title: SMC3au_G2_P2_rep1

description:
150 bp x 150 bp
35_SMC3au_G2_P2


title: A. burtoni, testes, rep2 [smallRNA-seq]


title: SMC3au_G2_P3_rep1

description:
150 bp x 150 bp
36_SMC3au_G2_P3


title: wt_Mnoc_P3_rep2

description:
150 bp x 150 bp
33_wt_Mnoc_P3


title: M. zebra, testes, rep1

description:
Mze_tes_rep1
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt


title: wt_Mnoc_P1_rep2

description:
150 bp x 150 bp
31_wt_Mnoc_P1


title: M. zebra, testes, rep2 [smallRNA-seq]


title: T. mauve, testes, rep2

description:
Tma_tes_rep2
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt


title: M. zebra, testes, rep1 [smallRNA-seq]


title: T. mauve, testes, rep1

description:
Tma_tes_rep1
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt


title: wt_Mnoc_P2_rep1

description:
150 bp x 150 bp
29_wt_Mnoc_P2


title: wt_Mnoc_P1_rep1

description:
150 bp x 150 bp
28_wt_Mnoc_P1


title: wt_Mnoc_P3_rep1

description:
150 bp x 150 bp
30_wt_Mnoc_P3


title: T. mauve, testes, rep2 [smallRNA-seq]


title: HCT116 Untreated CDK2mut EdU+BrdU BiolRep2

first: Michael

last: Boemo

department: Department of Pathology

description: R9.4.1 flowcells

data_processing:
Basecalling (Guppy v5.0.11)
Genome alignment (Minimap2 v2.17-r941)
BrdU and EdU detection (DNAscent v3.1.2)
Fork calling (DNAscent v3.1.2)
Assembly: chm13v2.0 (telomere-to-telomere)
Supplementary files format and content: bed files (fork calls)

organism: Homo sapiens

extract_protocol:
Nanobind CBB Big DNA Kit (SKU NB-900-001-01, Circulomics) and UHMW DNA Aux Kit (NB-900-101-01, Circulomics)
Ultra-Long DNA Sequencing Kit (SQK-ULK001, ONT) and Nanobind UL Library Prep Kit (NB-900-601-01, Circulomics)


title: wt_M_P3_rep2

description:
150 bp x 150 bp
24_wt_M_P3


title: wt_G2_P3_rep2

description:
150 bp x 150 bp
21_wt_G2_P3


title: A2058 ATRi EdU+BrdU BiolRep1

description: R9.4.1 flowcells

value: ATRi


title: wt_M_P1_rep2

description:
150 bp x 150 bp
22_wt_M_P1


title: A2058 ATRi EdU+BrdU BiolRep2

description: R9.4.1 flowcells


title: A2058 WEE1i EdU+BrdU BiolRep2

description: R9.4.1 flowcells


title: wt_M_P2_rep2

description:
150 bp x 150 bp
23_wt_M_P2


title: HCT116 Untreated WT EdU+BrdU BiolRep2

description: R9.4.1 flowcells


title: wt_Mnoc_P2_rep2

description:
150 bp x 150 bp
32_wt_Mnoc_P2


title: A2058 WEE1i EdU+BrdU BiolRep1

description: R9.4.1 flowcells


title: A2058 PARPi EdU+BrdU BiolRep2

description: R9.4.1 flowcells

value: PARPi


title: A2058 PARPi EdU+BrdU BiolRep1

description: R9.4.1 flowcells


title: HCT116 Untreated CDK2mut EdU+BrdU BiolRep1

description: R9.4.1 flowcells


title: A2058 Untreated EdU+BrdU BiolRep2

description: R9.4.1 flowcells


title: wt_M_P2_rep1

description:
150 bp x 150 bp
17_wt_M_P2


title: wt_M_P1_rep1

description:
150 bp x 150 bp
16_wt_M_P1


title: A2058 HU EdU+BrdU BiolRep1

description: R9.4.1 flowcells

value: HU


title: wt_G2_P1_rep2

description:
150 bp x 150 bp
19_wt_G2_P1


title: A2058 HU EdU+BrdU BiolRep2

description: R9.4.1 flowcells


title: HCT116 Untreated WT EdU+BrdU BiolRep1

description: R9.4.1 flowcells


title: wt_G2_P3_rep1

description:
150 bp x 150 bp
15_wt_G2_P3


title: SMC2au_M_P2_rep1

description:
150 bp x 150 bp
11_SMC2au_M_P2


title: NvecPlanula

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
10x scRNA-seq: Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline (version 4.0). Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using nematostella genome NV2. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters.
Assembly: NV2
Supplementary files format and content: single cell expression matrix in h5 format from 10X cellranger pipeline

organism: Nematostella vectensis

source_name: NvecPlanula sorted cells

extract_protocol:
300 planula larvae were transferred to a 1.5mL eppendorf tube and the normal culture media (12ppt artificial sea water) was removed and replaced with 500uL of calcium free, magnesium free 12ppt artificial sea water. After plaunla had dissociated the solution was passed through an 80um syringe filter to establish a single cell suspension. Cells were sorted with flow cytometry based on alive (DAPI-/Draq5+) or dead (DAPI+/Draq5+) which ultimately ended up being ~300,000 cells total. From there, the maximum number of cells were used for cDNA library prep which ended up being ~7,000.
The library construction follows 10X scRNA-seq protocols using the v2 kit.

value: planula

tag: protocol

value: 10X scRNA-seq


title: ASM_R3

city: Beaucouzé

first: Matthieu

last: Gaucher

address: 42 rue Georges Morel

department: SPE

country: France

institute: INRAE

data_processing:
The sequenced reads (ranging from 31.9 to 48 million read pairs per sample) were mapped on the reference transcriptional units from GDDH13 v1.1 using Salmon software (Patro et al., 2017)
Identification of differentially expressed genes (DEGs) was performed with EdgeR, including a Benjamini–Hochberg procedure to control the false discovery rate (FDR) (Love et al., 2014)
Assembly: MJAX00000000.1
Supplementary files format and content: tab-delimited file include raw counts values for each sample, logCPM and log2ratios for each comparison

organism: Malus domestica

source_name: leaf

growth_protocol: Plants were grown in individual pots (8 x 5.5 x 7 cm) under greenhouse conditions (natural photoperiod supplemented with artificial light if needed, 17°C night and 20–23°C day)

extract_protocol:
RNA was harvested using NucleoSpin RNA Plant (Macherey Nagel)
Libraries were generated using the Illumina mRNA Stranded protocol

treatment_protocol: Bion 50WG (ASM) and water were sprayed to runoff on entire plants with a spray gun. Plants received two treatments four days apart, and sampling for RNAseq analysis occurred 3 days after the second treatment

value: leaf

value: Golden delicious

value: Bion 50WG


title: SMC3-AID_CDK1as_subclone_1 (biol rep2)_CENP-A_ChIP

description: 100 bp

data_processing:
Remove adapters with Cutadapt-1.18 --minimum-length 20 --nextseq-trim=20
Align to galGal7b reference with bwa mem
Convert to coverage file with deeptools bamCoverage -bs 1 --normalizeUsing BPM
Assembly: GRCg7b
Supplementary files format and content: BigWig

growth_protocol: DMEM, 10% FBS, 1% Chicken serum, betamercaptoethanol, penicillin and streptmycin. Cells were culutured at 38C at 5% CO2.

extract_protocol:
A nuclear fraction of cells was digested with MNase and solubulised with 0.5M NaCl. CENP-A containing nucleosomes were immunoprecipitated with custom-made CENP-A antibody.
ChIP-seq libraries were prepared either using NEBNext Ultra II prep (WT, SMC2, SMC3) or KAPA Hyper prep (CAP-H, CAP-H2).

treatment_protocol: asynchronous growth mainting the concentration between 0.2-1 X10^6/ml

tag: Sex

value: female

tag: chip antibody

value: custome made anti CENP-A antibody


title: SMC2au_M_P1_rep1

description:
150 bp x 150 bp
10_SMC2au_M_P1


title: SMC2au_G2_P2_rep1

description:
150 bp x 150 bp
02_SMC2au_G2_P2


title: wt_G2_P2_rep1

description:
150 bp x 150 bp
14_wt_G2_P2


title: ASM_R2


title: SMC2au_G2_P3_rep1

description:
150 bp x 150 bp
03_SMC2au_G2_P3


title: Water_R3

value: water


title: SMC3-AID_CDK1as_subclone_1(biol rep1)_CENP-A_ChIP

description: 100 bp

value: Bursa


title: SMC2au_G2_P1_rep1

description:
150 bp x 150 bp
01_SMC2au_G2_P1

value: lymphoblast


title: wt_M_P3_rep1

description:
150 bp x 150 bp
18_wt_M_P3

value: female (ZW)


title: Water_R1


title: Water_R2


title: SMC2au_M_P3_rep1

description:
150 bp x 150 bp
12_SMC2au_M_P3


title: ASM_R1


title: SMC2-AID_CDK1as_subclone_1 (biol rep2)_CENP-A_ChIP

description: 100 bp


title: A2058 Untreated EdU+BrdU BiolRep1

description: R9.4.1 flowcells


title: MM106_Ea 24hpi_R3

data_processing:
The sequenced reads (ranging from 21.5 to 60 million read pairs per sample) were mapped on the reference transcriptional units from GDDH13 v1.1 using Salmon software (Patro et al., 2017)
Identification of differentially expressed genes (DEGs) was performed with EdgeR, including a Benjamini–Hochberg procedure to control the false discovery rate (FDR) (Love et al., 2014)
Assembly: MJAX00000000.1
Supplementary files format and content: tab-delimited file include raw counts values for each sample, logCPM and log2ratios for each comparison

growth_protocol: Plants were grated on MM106 roostock and grown in individual potss under greenhouse conditions (natural photoperiod supplemented with artificial light if needed, 17°C night and 20–23°C day)

treatment_protocol: Inoculation was performed by vaccum infiltration as described in Dugé de Bernonville et al., 2012. Briefly the top young leaves of each shoot were infiltrated by dipping the shoot itself into the bacterial suspension or mock. Plants were then cultivated under the growth conditions

value: Ea 0.01% Silwet


title: SMC2-AID_CDK1as_subclone_1(biol rep1)_CENP-A_ChIP

description: 100 bp


title: MM106_Ea 24hpi_R2


title: wt_G2_P1_rep1

description:
150 bp x 150 bp
13_wt_G2_P1


title: MM106_Ea 24hpi_R1


title: MM106_mock 24hpi_R3

value: water 0.01% Silwet


title: Caenorhabditis elegans,20℃,  after feeding 5mM tryptophan for 36 hours in L4 period, rep3

city: Kaifeng

first: Shanqing

last: Zheng

address: 1 Jinming Avenue North, Longting District,  School of Basic Medical Sciences, Henan University

country: China

institute: Henan university

data_processing:
Illumina Casava1.7 software used for base-calling
Sequenced reads were trimmed for adaptor sequence. and masked for low-complexity or low-quality sequence. then mapped to WBcel235 whole genome using bowtie v0.12.2 with parameters
The transcript abundances for each sample was estimated with StringTie（1.3.3）
The FPKM value for gene and transcript level was calculated through a protocol from Chepelev et al., Nucleic Acids Research,2009.
Assembly: C. elegans genome version WBcel235 was used as the reference.
Supplementary files format and content: The txt format file contains the FPKM value of  expression gene.

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: Synchronize the worms, culture the collected eggs in M9 and incubate to L1 at 20 °C, transfer to NGM plates and feed to the L4 stage.

extract_protocol: RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1ug of total RNA for the construction

treatment_protocol: At L4 period, the experimental group worms are fed 5 mM tryptophan for 36 h.

value: whole body

tag: age

value: young adult

value: hermaphrodite

value: WT

value: 5mM tryptophan was fed for 36 hours from the L4 period


title: Caenorhabditis elegans,20℃,  after feeding 5mM tryptophan for 36 hours in L4 period, rep2


title: MM106_mock 24hpi_R2


title: MM106_mock 24hpi_R1


title: Caenorhabditis elegans,20℃,  after feeding 5mM tryptophan for 36 hours in L4 period, rep1


title: wt_G2_P2_rep2

description:
150 bp x 150 bp
20_wt_G2_P2

value: Oligo pool 2


title: Caenorhabditis elegans,20℃, 36 hours after L4 period, rep3

value: control


title: Caenorhabditis elegans,20℃, 36 hours after L4 period, rep1


title: K562_U6DDR_naive_Rep3

city: Stanford

first: Jinglong

last: Wang

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

department: Radiation Oncology

institute: Stanford University

data_processing:
PCR-mediated template switching, involved the extraction and merging of barcodes from the paired-end sequencing library based on sequencing identification (ID). Paired barcodes underwent pairwise alignment and were compared with a reference barcode list to determine matched, switched, and randomly occurring errors.
The mapping of each paired library to the reference DNA template was executed using CRISPResso2 and stored in BAM files.
The ID and Cigar information were extracted and generated into TXT files, which were then merged with the matched file containing barcodes identified by ID.
Gene information was incorporated based on the sgRNA spacer sequence.
For the analysis of repair outcomes, it was assumed that the Double-Strand Breaks (DSB) occurred within ±10bps of the ideal break site. This implies that the deletion window must overlap with the DSB window, and all insertions must reside within this DSB window.
Assembly: hg19, pMCB320-DDR, pMCB320-RuDDR
Supplementary files format and content: tab delimited text files contain the pairwise alignment information including: the index, the barcode 1 (sequence_x), sequence identity (ID), length of barcode 1 (len_x), the barcode 2 or the spacer (sequence_y), length of barcode 2 (len_y), the reverse complement of barcode 2 (sequence_y_rcp) and the alignment score between barcode 1 and the barcode 2 (Align_score).
Supplementary files format and content: tab delimited text files contain the filtered, annotated mapping information including: the Index, the sequencing identity (ID), the barcode 1 (barcode), the barcode 2 or sgRNA spacer (seq_exp), the alignment score between barcode 1 and barcode 2 (Align_score), the gene name (Symbol), the mapping to a 362bp region of interest in the reference template (Cigar), the length of deletion (D_length),  the position of deletion (D_location), the length of insertion (I_insertion), the position of insertion (I_location).
Library strategy: Dual-barcode Repair-Seq

growth_protocol: K562-iCas9-DDR cell line was cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
DDR libraries were constructed through a two-step PCR process. In the initial PCR, outer layer primers (DDR-lib-F1 and DDR-lib-R1) were employed to amplify the regions of interest. Subsequently, in the second PCR, I5-DDR and I7-DDR primers were used to tag the libraries, which were then purified through electrophoresis and a gel-extraction kit.

treatment_protocol: G1/G0-arrested K562-iCas9-DDR cell lines were treated by 50 μM Palbociclib. The cycling and G1/G0-arrested cells were transduced with Cas12a plus DDR1-crRNA nucleoproteins to generated twined  DSBs in different compound-treated conditions.

value: lymphoblast cells

value: Nucleofection

tag: dsb induction

tag: polymerase

value: Taq


title: Evereste_mock 24hpi_R2

value: leaf

value: Evereste


title: Evereste_Ea 24hpi_R2


title: Evereste_Ea 24hpi_R3


title: Caenorhabditis elegans,20℃, 36 hours after L4 period, rep2


title: Evereste_mock 24hpi_R3


title: Evereste_mock 24hpi_R1


title: K562_U6DDR_naive_Rep2


title: K562_U6DDR_naive_Rep1


title: WT_CDK1as_subclone_1 (biol rep2)_CENP-A_ChIP

description: 100 bp

value: Bursa

value: female

value: custome made anti CENP-A antibody


title: MM106_Ea 6hpi_R3

value: Ea 0.01% Silwet


title: MM106_Ea 6hpi_R1


title: K562_U6DDR_G1_CLV_Rep3


title: MM106_Ea 6hpi_R2


title: K562_U6DDR_G1_CLV_Rep1


title: K562_U6DDR_Doxy_Rep3


title: K562_U6DDR_G1_CLV_Rep2


title: WT_CDK1as_subclone_1(biol rep1)_CENP-A_ChIP

description: 100 bp

data_processing:
Extend single end reads to 200bp
Remove adapters with Cutadapt-1.18 --minimum-length 20 --nextseq-trim=20
Align to galGal7b reference with bwa mem
Convert to coverage file with deeptools bamCoverage -bs 1 --normalizeUsing BPM
Assembly: GRCg7b
Supplementary files format and content: BigWig

value: lymphoblast


title: MM106_mock 6hpi_R2

value: water 0.01% Silwet


title: K562_U6DDR_Doxy_Rep2


title: MM106_mock 6hpi_R1


title: MM106_mock 6hpi_R3


title: K562_U6DDR_Doxy_Rep1


title: K562_U6DDR_Cycing_CLV_Rep3


title: Evereste_Ea 6hpi_R3


title: Evereste_Ea 24hpi_R1


title: Evereste_Ea 6hpi_R2


title: K562_U6DDR_Cycing_CLV_Rep1


title: K562_U6DDR_Cycing_CLV_Rep2


title: Evereste_mock 6hpi_R3


title: LNCaP_e4_2_H3K27ac_ChIP

city: Salt Lake City

first: Xiaoyang

last: Zhang

state: Utah

address: 1950 Circle of Hope Drive

department: Oncological Sciences

institute: University of Utah

data_processing:
Bowtie2 to align sequencing reads
MACS2 to identify ChIP-seq peaks and calculate Signal Per Million Reads (SPMR)
Assembly: hg19
Supplementary files format and content: bigWig (bw)

source_name: LNCaP-clone FGC

extract_protocol:
Chromatin immunoprecipitation using antibodies to enrich DNA fragments
NEBNext DNA Ultra II library prep kit (E7645S)

value: LNCaP-clone FGC

value: Prostate adenocarcinoma cell line

value: H3K27ac (Abcam ab4729)


title: Evereste_mock 6hpi_R2


title: Evereste_Ea 6hpi_R1


title: Evereste_mock 6hpi_R1


title: LNCaP_e3_2_H3K27ac_ChIP


title: MM106_T0_R3


title: LNCaP_e3_1_H3K27ac_ChIP


title: MM106_T0_R2


title: 8wLD+21wLD@4C+5dLD_rep2

city: Köln

first: Maria

last: Albani

address: Carl-von-Linné-Weg 10

department: Botanical institute

country: Germany

institute: University of Cologne

description:
Mishra_RNA-Seq_GEO_Count.xlsx
Mishra_RNA-Seq_GEO_Comparison.xlsx

data_processing:
The reads were mapped to the Arabis alpina reference genome (Assembly Version 5) using HISAT2 package with default settings. The SAM files obtained after mapping were converted into BAM files.
Genes were assembled and quantified in each sample using StringTie package. The raw gene count was obtained by feeding the .gtf file to a python script (prepDE.py) obtained from http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual.
The raw gene counts table was further analysed with DESeq2 to obtain differentially expressed genes.
Differentially expressed genes within 2 conditions with a fold change of 2 and a p-value significance <0.05 were analysed further.
Genome_build: Arabis alpina ( NCBI ID: 17813)
Supplementary_files_format_and_content: Excel sheets containing the count of each gene in each replicate of each sample and the normalised abundance measurement from DESeq2.

molecule: polyA RNA

organism: Arabis alpina

source_name: main stem

growth_protocol: Plants were grown for 8 weeks in long day conditions (LD, 16h light at 20°C, 8h dark at 18°C) followed by extended exposure to cold (4°C) in LD conditions for different durations. The plants were then shifted back to greenhouse LD conditions.

extract_protocol:
RNA was isolated using RNeasy Plant RNA isolation kit (Qiagen) according to the manufacturer's instructions.
The libraries were prepared from 1 µg total RNA with RNA integrity number >8 (Bioanalyzer; Agilent) using the NEBNext Ultra Directional II RNA Library Prep Kit for Illumina (New England Biolabs) at the Cologne Genome Centre and sequencing was carried out using a HiSeq3000 (Illumina)  generating 1 x 150 bp single reads.

treatment_protocol: After 8 weeks in LD (16h light at 20°C, 8h dark at 18°C) conditions, plants were exposed to 4, 8, 12, 16 and 21 weeks of cold (4°C). After cold exposure, plants were transfered to LD conditions.

tag: arabis alpina ecotype

value: Pajares

tag: duration of cold exposure

value: 21 weeks

tag: days in ld after cold exposure

tag: position of tissue collection

value: 2 cm of the main stem below the rosette


title: 8wLD+21wLD@4C+5dLD_rep3


title: 8wLD+21wLD@4C+5dLD_rep1


title: MM106_T0_R1


title: 8wLD+21wLD@4C_rep3


title: Evereste_T0_R2


title: LNCaP_e4_1_H3K27ac_ChIP


title: Evereste_T0_R3


title: 8wLD+21wLD@4C_rep2


title: A. calliptera, male brain, rep2

description:
Aca_mbra_rep2
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt

organism: Astatotilapia calliptera

source_name: Brain (male)

value: Brain (male)

value: wild-type


title: 8wLD+21wLD@4C_rep1


title: A. calliptera, male brain, rep1

description:
Aca_mbra_rep1
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt


title: 8wLD+16wLD@4C+5dLD_rep3

value: 16 weeks


title: A. calliptera, female brain, rep3

description:
Aca_fbra_rep3
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt

source_name: Brain (female)

value: Brain (female)


title: A. calliptera, female brain, rep2

description:
Aca_fbra_rep2
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt


title: LNCaP_NT1_H3K27ac_ChIP


title: Evereste_T0_R1

value: leaf

value: Evereste


title: A. calliptera, female brain, rep1

description:
Aca_fbra_rep1
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt


title: 8wLD+16wLD@4C+5dLD_rep1


title: A. calliptera, testes, rep4

description:
Aca_tes_rep4
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt
rawCounts_mRNA_GenesAndTEs_Acal.txt
NormCounts_mRNA_TEs_Acal.txt
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt

value: Testes


title: 8wLD+16wLD@4C+5dLD_rep2


title: A. calliptera, testes, rep3

description:
Aca_tes_rep3
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt
rawCounts_mRNA_GenesAndTEs_Acal.txt
NormCounts_mRNA_TEs_Acal.txt
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt


title: A. calliptera, male brain, rep3

description:
Aca_mbra_rep3
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt


title: 8wLD+16wLD@4C_rep2


title: 8wLD+16wLD@4C_rep3


title: 8wLD+12wLD@4C+5dLD_rep3

value: 12 weeks


title: A. calliptera, ovary, rep4

description:
Aca_ov_rep4
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt
rawCounts_mRNA_GenesAndTEs_Acal.txt
NormCounts_mRNA_TEs_Acal.txt
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt

value: Ovary


title: A. calliptera, testes, rep1

description:
Aca_tes_rep1
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt
rawCounts_mRNA_GenesAndTEs_Acal.txt
NormCounts_mRNA_TEs_Acal.txt
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt


title: 8wLD+12wLD@4C+5dLD_rep2


title: A. calliptera, ovary, rep1

description:
Aca_ov_rep1
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt
rawCounts_mRNA_GenesAndTEs_Acal.txt
NormCounts_mRNA_TEs_Acal.txt
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt


title: 8wLD+12wLD@4C+5dLD_rep1


title: 8wLD+12wLD@4C_rep3


title: A. calliptera, ovary, rep3

description:
Aca_ov_rep3
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt
rawCounts_mRNA_GenesAndTEs_Acal.txt
NormCounts_mRNA_TEs_Acal.txt
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt


title: 8wLD+12wLD@4C_rep2


title: 8wLD+12wLD@4C_rep1


title: A. calliptera, testes, rep4 [smallRNA-seq]


title: A. calliptera, testes, rep3 [smallRNA-seq]


title: 8wLD+8wLD@4C_rep1

value: 8 weeks


title: A. calliptera, ovary, rep3 [smallRNA-seq]


title: 8wLD+8wLD@4C_rep3


title: A. calliptera, testes, rep2

description:
Aca_tes_rep2
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt
rawCounts_mRNA_GenesAndTEs_Acal.txt
NormCounts_mRNA_TEs_Acal.txt
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt


title: A. calliptera, testes, rep1 [smallRNA-seq]


title: 8wLD+4wLD@4C_rep2

value: 4 weeks


title: 8wLD+4wLD@4C_rep1


title: 8wLD+4wLD@4C_rep3


title: A. calliptera, muscle, rep2 [smallRNA-seq]

source_name: Muscle

value: Muscle


title: 8wLD_rep3

value: 0 weeks


title: 8wLD+16wLD@4C_rep1


title: A. calliptera, ovary, rep2 [smallRNA-seq]


title: vestibular schwannoma 2

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

institute: University of Birmingham

library_source: transcriptomic single cell

data_processing:
CellRanger v7.0 (10x genomics)
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5

source_name: vestibular schwannoma tumor

extract_protocol: 10x 3’ Single Index protocol

value: vestibular schwannoma tumor

value: unknown


title: vestibular schwannoma 3


title: 8wLD_rep1

value: Pajares


title: vestibular schwannoma 1


title: A. calliptera, ovary, rep2

description:
Aca_ov_rep2
rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt
NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt
rawCounts_mRNA_GenesAndTEs_Acal.txt
NormCounts_mRNA_TEs_Acal.txt
rawCounts_mRNA_Acal_brain_gonads.txt
lengthScaledTPM_mRNA_Acal_brain_gonads.txt


title: infected_in_vivo

city: Philadelphia

first: Katelyn

middle: Ann

last: Walzer

state: PA

address: 380 South University Avenue

department: Pathobiology

institute: University of Pennsylvania

description: 10x Chromium Single Cell 3’ Library v3 chemistry, NextSeq 500/550 High Output Kit v2.5 (75 cycles)

data_processing:
Cell Ranger 3.1.0 was used to process sequencing reads and build a reference genome for C. parvum Iowa II (VEuPathDB, release 46) or C. parvum IOWA-ATCC (for inclusion of long non-coding RNAs). Processed reads from each sample were aligned to this reference genome and produced filtered feature-barcode matrices, which are the features (tsv), barcodes (tsv), and matrix (mtx) files listed in this submission.
Seurat 3.1.4 was used for filtering, normalization, clustering, UMAP visualization, and marker identification (FindAllMarkers: only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25; adjacent clusters with similar marker genes were combined).
The command line tool velocyto and package velocyto.R were used to estimate and visualize RNA velocity.
Monocle3 was used to produce pseudotime trajectories.
Version 46 of the Cryptosporidium parvum Iowa II reference from VEuPathDB (used for most analyses) or Cryptosporidium parvum IOWA-ATCC from Baptista RP et al., Genome Res., 2022 (used for analyses with lncRNAs)
The filtered_feature_bc_matrix (Cell Ranger 3.1.0 output) consists of features (tsv), barcodes (tsv), and matrix (mtx) files. The features (tsv) file is the same for all samples. The RDS files contain the Seurat objects for the Cryptosporidium single-cell atlases (asexual, total life cycle, and total life cycle with lncRNAs), with corresponding csv files containing the metadata information.

organism: Cryptosporidium parvum

source_name: protozoa

growth_protocol: Cell cultures and IFN-gamma KO mice were infected with the tdNeon RPL22 HA parasite strain. HCT-8 cells in a 6-well plate were infected with 500,000 (24 hours), 300,000 (36, 42, and 46 hours), and 200,000 (54 hours) oocysts, with wells set up in triplicate for the 24-, 36-, 42-, and 54-hour timepoints. Three IFN-gamma KO mice were infected with 20,000 oocysts, and transgenic parasites were selected with 16 mg/mL of paromomycin in drinking water. Mice were euthanized on day 6 of infection, and epithelial cells were obtained from the small intestine of the most highly infected mouse.

extract_protocol:
Infected cells from culture and mice were sorted into 500 µL of 40% CCS complete media, which was further diluted in PBS (up to 1 mL total volume) after sorting. After centrifugation and resuspension in 1x PBS (calcium and magnesium free) containing 0.04% weight/volume BSA (400 µg/mL), cells were loaded onto a chromium chip for encapsulation via the 10x Genomics platform.
10x Chromium Single Cell 3’ Library v3 chemistry was used and manufacturer’s instructions were followed for cDNA amplification and library construction. The NextSeq 500/550 High Output Kit v2.5 (75 cycles) was used to obtain paired-end reads from an Illumina NextSeq 500 sequencer.

tag: source

value: Cryptosporidium parvum infected mouse cells

tag: background strain

value: Cryptosporidium parvum Iowa II (Bunchgrass Farms)

value: tdNeon RPL22 HA

tag: cell preparation

value: single cell

value: protozoa


title: A. calliptera, testes, rep2 [smallRNA-seq]

tag: tissue

tag: genotype

value: wild-type


title: crypto46hrs

value: Cryptosporidium parvum infected HCT-8 cells

tag: cell type


title: 8wLD+8wLD@4C_rep2

value: 2 cm of the main stem below the rosette


title: KW148-gb102c1

city: San Francisco

first: Kristen

last: Seim

state: CA

address: 201 Haskins Way

institute: GraphiteBio

description:
bc1002--bc1002.bam
PacBio No-Amp Targeted sequencing
PacBio_Results.csv

data_processing:
Instrument model: PacBio Sequel IIe
FASTQ files were used as input files to align to chromosome 11 (hg38) by minimap2 (v.2.24)
Assembly: hg38
Supplementary files format and content: csv file with variant calling

source_name: blood

extract_protocol:
high molecular weight genomic DNA was extracted, and 5' and 3' phosphates were removed. The b-globin gene cluster was enriched by Cas9-RNPs digestion of two 10 kb fragments. PacBio SMRTbells were ligated to fragments, pooled and sequenced on a PacBio Sequel IIe
PacBio libraries were generated using the No Amp protocol

value: blood

value: CD34+ cells

value: WT

tag: treatment


title: KW148-gb102c2

description:
bc1008--bc1008.bam
PacBio No-Amp Targeted sequencing
PacBio_Results.csv


title: BT-060-gb102c2

description:
bc1018--bc1018.bam
PacBio No-Amp Targeted sequencing
PacBio_Results.csv


title: crypto54hrs


title: A. calliptera, ovary, rep1 [smallRNA-seq]

data_processing:
The data resides within R1 so R2 was discarded. CutAdapt v1.15 (Martin, 2011) was used to remove adapters and reads shorter than 18 nucleotides with options -a TGGAATTCTCGGGTGCCAAGG   minimum-length 18 -o.
We selected small RNAs in the piRNA size range, between 24 and 35 nucleotides long, for further analysis. We have done this size selection using CutAdapt v1.15 (Martin, 2011) with options ‑‑minimum-length 24 --maximum-length 35.
We mapped the 24-35 nucleotide long reads to the genome using STAR v2.5.4b (Dobin et al., 2013), with options --outTmpDir --genomeDir   --readFilesIn --readFilesCommand zcat   outMultimapperOrder Random --outFilterMultimapNmax 100   outFilterMismatchNmax 2 --alignIntronMax 1 --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --winAnchorMultimapNmax 100 --alignEndsType EndToEnd   scoreDelOpen -10000 --scoreInsOpen -10000 --outSAMmultNmax 1   outFileNamePrefix. Reads from Lake Malawi cichlid species (A. calliptera, M. zebra, T. sp. "mauve") were all mapped to the A. calliptera genome fAstCal1.2. A. burtoni, P. nyererei, and O. niloticus reads were mapped to their genomes: AstBur1.0, PunNye1.0, and  O_niloticus_UMD_NMBU respectively. All these genomes are available at Ensembl.
To quantify piRNA counts mapping to TEs, we used featureCounts v1.6.0 (Liao et al., 2014) with options -a -o -t exon -M. The 24-35 nucleotide long BAM file was used as input. For Lake Malawi cichlids, featureCounts analysis was performed twice, using A. calliptera default and curated TE annotations. DESeq2 (Love et al., 2014) and custom scripts  were used to calculate normalized counts, generate plots and conduct statistical tests on an R framework (R Core Team, 2021).
Assembly: fAstCal1.2; AstBur1.0; PunNye1.0; O_niloticus_UMD_NMBU
Supplementary files format and content: Abur_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to  TEs in each A. burtoni sample.
Supplementary files format and content: Malawi_sRNA_NormTEcounts_CuratedAnnotation_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to TEs in each Lake Malawi cichlid sample. Using a curated TE annotation.
Supplementary files format and content: Malawi_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to TEs in each Lake Malawi cichlid sample.
Supplementary files format and content: Onil_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to  TEs in each O. niloticus sample.
Supplementary files format and content: Pnye_sRNA_NormTEcounts_GEO.txt. Tab-delimited file includes DESeq2 normalized counts for piRNAs mapping to  TEs in each P. nyererei sample.

value: Ovary


title: BT-060-gb101

description:
bc1017--bc1017.bam
PacBio No-Amp Targeted sequencing
PacBio_Results.csv


title: crypto42hrs


title: gb102 Engraftment study; Donor 328 unedited sample

description:
328_unedited
PacBio No-Amp Targeted sequencing
PacBio_Results.csv

value: unedited


title: crypto24hrs


title: gb102 Engraftment study; Donor 328 HBB only

description:
328_HBB
PacBio No-Amp Targeted sequencing
PacBio_Results.csv

value: HBB only


title: Male_in_vitro_3

description: RNeasy minikit, Clontech SMART-seq HT kit, Illumina Nextera XT Library Prep Kit

data_processing:
Fastq files were pseudoaligned to the Cryptosporidium parvum Iowa II reference transcriptome (version 46, VEuPathDB) using Kallisto v.0.45.0
Kallisto transcript counts were imported into R using the Bioconductor package tximport
Expression data was normalized using the TMM method in the function calcNormFactors from the package edgeR
Differentially expressed genes (log2 fold-change ≥ 1 and p-value ≤ 0.01) were identified by linear modeling and Bayesian statistics using the limma package
Version 46 of the Cryptosporidium parvum Iowa II reference from VEuPathDB (used for most analyses) or Cryptosporidium parvum IOWA-ATCC from Baptista RP et al., Genome Res., 2022 (used for analyses with lncRNAs)
Tab-delimited text files include log2 counts per million (CPM) values for each sample

growth_protocol: HCT-8 cells grown in a 6-well plate were infected with 300,000 AP2-M tdNeon oocysts per well (four biological replicates) for 48 hours at 5% CO2 and 37º C

extract_protocol:
10,000 tdNeon positive cells were sorted directly into 350 µL of RLT lysis buffer from an RNeasy Mini Kit (Qiagen), and RNA was isolated according to manufacturer’s instructions
The Clontech SMART-seq HT kit was used for cDNA synthesis, and the Illumina Nextera XT Library Prep Kit was used to prepare libraries for sequencing

value: AP2-M 5' UTR tdNeon

value: bulk


title: gb102 Engraftment study; Donor 328 RNP only

description:
328_RNP
PacBio No-Amp Targeted sequencing
PacBio_Results.csv

value: RNP


title: crypto36hrs


title: gb102 Engraftment study; Donor 1125 RNP only

description:
1125_RNP
PacBio No-Amp Targeted sequencing
PacBio_Results.csv


title: Male_in_vitro_2


title: Male_in_vitro_1


title: 8wLD_rep2

description:
Mishra_RNA-Seq_GEO_Count.xlsx
Mishra_RNA-Seq_GEO_Comparison.xlsx

value: Pajares

value: 0 weeks


title: Male_in_vitro_4

value: Cryptosporidium parvum Iowa II (Bunchgrass Farms)


title: gb102 Engraftment study; Donor 1125 HBB only

description:
1125_HBB
PacBio No-Amp Targeted sequencing
PacBio_Results.csv


title: EC_WT,  mRNA-derived cDNA

city: Seattle

first: Geoffrey

middle: R

last: Hill

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

description: 10x genomics

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression) was performed using the 10x genomics Cell Ranger pipeline  and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, clustering, differential gene expression analysis).
The demultiplexing, barcode processing, cell counting were made using cellranger software -7.0.0
Assembly: mm10
Supplementary files format and content: normalized RNA  count matrices, cell metadata, cellranger bams

source_name: Liver

extract_protocol:
Cells were isolated from liver following enzymatic digestion, pooled per group (n = 3 mice), stained with CD3-PECy7, CD45-BUV395, TER119-APC and 7-AAD and sort-puried to CD31+ endothelial cells.
Samples were resuspended at 1000 cells/uL and libraries  were  generated  using  the Chromium Single Cell 5' Reagent Kits User Guide (v2 Chemistry Dual Index) following the manufacturer’s protocol (CG000331, Pleasanton, CA). Final library quality was assessed using the Tapestation 4200 (Agilent, Santa Clara, CA) and libraries were quantified by Qubit dsDNA kit on Denovix( spectrometer/flurometer) .Pooled libraries were then subjected to paired-end Illumina sequencing according  to the  manufacturer’s  protocol

value: Liver

value: endothelial cells

value: Mice transplanted with BM + T cells from allogeneic WT donors


title: EC_TCD,  mRNA-derived cDNA

description: 10x genomics

value: Mice transplanted with TCD BM from allogeneic WT donors


title: O. niloticus, ovary, rep3

description:
Oni_ov_rep3
rawCounts_mRNA_GenesAndTEs_Onil.txt
NormCounts_mRNA_TEs_Onil.txt

data_processing:
Illumina adapters and reads with low-quality calls were filtered out with Trimmomatic v0.39 (Bolger et al., 2014) using options SLIDINGWINDOW:4:28 MINLEN:36.
We mapped trimmed reads to the genome, using STAR v2.5.4b (Dobin et al., 2013) with options --outTmpDir --readFilesCommand zcat ‑‑genomeDir ‑‑readFilesIn {R1} {R2} --outSAMtype BAM SortedByCoordinate ‑‑outFilterType BySJout --outFilterMultimapNmax 150 ‑‑winAnchorMultimapNmax 150 --alignSJoverhangMin 8 --alignSJDBoverhangMin 3 ‑‑outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 10000000 --alignMatesGapMax 100000000 --outFileNamePrefix. Reads from Lake Malawi cichlid species (A. calliptera, M. zebra, T. sp. "mauve") were all mapped to the A. calliptera genome fAstCal1.2. A. burtoni, P. nyererei, and O. niloticus reads were mapped to their genomes: AstBur1.0, PunNye1.0, and  O_niloticus_UMD_NMBU respectively. All these genomes are available at Ensembl.
The resulting BAM files were used as inputs for TEtranscripts v2.2.1 (Jin et al., 2015) with options -t -c --GTF --TE --stranded reverse ‑‑project --SortByPos.
For A. calliptera samples, gene expression (without TEs) was quantified from trimmed reads using salmon v1.5.1 (Patro et al., 2017), with options --seqBias --gcBias - validateMappings -l A -1 ‑2 -o -i.
DESeq2 (Love et al., 2014) and custom scripts were used to calculate log-normalized and TPM counts, generate plots and conduct statistical tests on an R framework (R Core Team, 2021).
Assembly: fAstCal1.2; AstBur1.0; PunNye1.0; O_niloticus_UMD_NMBU
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Acal.txt: Tab-delimited file includes raw counts for genes and TEs in each A. calliptera sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Acal.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each A. calliptera sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Malawi_curatedTEAnnotation.txt: Tab-delimited file includes raw counts for genes and TEs in each Lake Malawi cichlid sample. Output of TEtranscripts, using a curated TE annotation.
Supplementary files format and content: NormCounts_mRNA_TEs_Malawi_curatedTEAnnotation.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each Lake Malawi cichlid sample. Using a curated TE annotation.
Supplementary files format and content: rawCounts_mRNA_Acal_brain_gonads.txt: Tab-delimited file includes raw counts in each A. calliptera sample. From Salmon output.
Supplementary files format and content: lengthScaledTPM_mRNA_Acal_brain_gonads.txt: Tab-delimited file includes length scaled TPM counts in each A. calliptera sample. From Salmon output.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Abur.txt: Tab-delimited file includes raw counts for genes and TEs in each A. burtoni sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Abur.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each A. burtoni sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Pnye.txt: Tab-delimited file includes raw counts for genes and TEs in each P. nyererei sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Pnye.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each P. nyererei sample.
Supplementary files format and content: rawCounts_mRNA_GenesAndTEs_Onil.txt: Tab-delimited file includes raw counts for genes and TEs in each O. niloticus sample. Output of TEtranscripts.
Supplementary files format and content: NormCounts_mRNA_TEs_Onil.txt: Tab-delimited file includes DESeq2 normalized counts for TEs in each O. niloticus sample.

organism: Oreochromis niloticus

value: wild-type


title: O. niloticus, testes, rep3

description:
Oni_tes_rep3
rawCounts_mRNA_GenesAndTEs_Onil.txt
NormCounts_mRNA_TEs_Onil.txt

value: Testes


title: O. niloticus, testes, rep1

description:
Oni_tes_rep1
rawCounts_mRNA_GenesAndTEs_Onil.txt
NormCounts_mRNA_TEs_Onil.txt


title: O. niloticus, ovary, rep1

description:
Oni_ov_rep1
rawCounts_mRNA_GenesAndTEs_Onil.txt
NormCounts_mRNA_TEs_Onil.txt


title: O. niloticus, testes, rep3 [smallRNA-seq]

extract_protocol:
Tissue pieces were transferred to BeadBug tubes prefilled with 0.5 mm Zirconium beads (Merck, #Z763772) and 500-600 µl of TRIzol (Life Technologies, #15596026) was added to the tubes and mixed vigorously. Afterwards, we conducted the homogenisation using a BeadBug microtube homogeniser (Sigma, #Z764140) at approximately 4oC (in cold room). Each sample was homogenised with five BeadBug runs at maximum speed (4000 rpm) for 60 seconds each. Supernatant was then removed into a clean 1.5 mL tube. Centrifuged the lysates again, this time at maximum speed (approximately 21,000 G) for 5 minutes at 4oC. Transferred supernatant into a clean tube without disturbing the pellet and tissue debris. Mixed supernatant thoroughly 1:1 with 100% ethanol, pipetted the mix into a column provided in the Direct-zol RNA Miniprep Plus kit (Zymo Research, #R2072) and followed manufacturer’s instructions, using the recommended in-column DNase I treatment.
Samples were processed according to the NEXTFLEX® Small RNA-Seq Kit v4 with UDIs (PerkinElmer, #NOVA-5132-32) with a 1 µg starting input and 12 cycles of PCR. Samples were then pooled in equimolar amounts according to the TapeStation results and sequenced on a Novaseq 6000 system (PE50 on one lane of an SP Flowcell).


title: O. niloticus, ovary, rep2

description:
Oni_ov_rep2
rawCounts_mRNA_GenesAndTEs_Onil.txt
NormCounts_mRNA_TEs_Onil.txt

extract_protocol:
Tissue pieces were transferred to BeadBug tubes prefilled with 0.5 mm Zirconium beads (Merck, #Z763772) and 500-600 µl of TRIzol (Life Technologies, #15596026) was added to the tubes and mixed vigorously. Afterwards, we conducted the homogenisation using a BeadBug microtube homogeniser (Sigma, #Z764140) at approximately 4oC (in cold room). Each sample was homogenised with five BeadBug runs at maximum speed (4000 rpm) for 60 seconds each. Supernatant was then removed into a clean 1.5 mL tube. Centrifuged the lysates again, this time at maximum speed (approximately 21,000 G) for 5 minutes at 4oC. Transferred supernatant into a clean tube without disturbing the pellet and tissue debris. Mixed supernatant thoroughly 1:1 with 100% ethanol, pipetted the mix into a column provided in the Direct-zol RNA Miniprep Plus kit (Zymo Research, #R2072) and followed manufacturer’s instructions, using the recommended in-column DNase I treatment.
Quality control, library preparation (directional, with poly-A enrichment), and mRNA sequencing (Illumina, PE150) was performed by Novogene. A. calliptera brain libraries and P.nyererei gonad libraries were prepared differently with the following protocol. We used 50-250 ng of total RNA for library production with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490), in conjunction with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, #E7760) and the NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB #E6440). Samples were then pooled in equimolar amounts and sequenced on a NovaSeq 6000 system (PE150 on one lane of an S1 Flowcell).


title: gb102 Engraftment study; Donor 1125 unedited sample

description:
1125_Unedited
PacBio No-Amp Targeted sequencing
PacBio_Results.csv

value: blood

value: CD34+ cells


title: O. niloticus, testes, rep2 [smallRNA-seq]


title: EC_IfngKO,  mRNA-derived cDNA

description: 10x genomics

value: Mice transplanted with BM + T cells from allogeneic Ifng KO donors


title: O. niloticus, testes, rep1 [smallRNA-seq]


title: O. niloticus, ovary, rep3 [smallRNA-seq]

value: Ovary


title: O. niloticus, ovary, rep1 [smallRNA-seq]


title: O. niloticus, ovary, rep2 [smallRNA-seq]


title: O. niloticus, testes, rep2

description:
Oni_tes_rep2
rawCounts_mRNA_GenesAndTEs_Onil.txt
NormCounts_mRNA_TEs_Onil.txt


title: MouseTL_CDAA_4

type: RNA

city: Lille

first: Ludivine

last: Clavreul

address: Bd du Pr Jules Leclecq

institute: INSERM UMR1011

description: Transcriptomic TL CDAA

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on Clariom S Assay, mouse Chip. GeneChips were washed and stained in the Affymetrix Fluidics.

scan_protocol: Affymetrix GeneChip Scanner 7G and Affymetrix GeneChip Command Console software (AGCC).

data_processing: RMA and scale intensity Normalization with GC correction using GIANT module on Galaxy (Galaxy tool ID : testtoolshed.g2.bx.psu.edu/repos/vandelj/giant_gsea_format/giant_gsea_format/0.2.0  ). The data obtained are log2-transformed.

label: biotin

source_name: C57Bl6 adult male mouse

label_protocol: RNA were processed using Affymetrix GeneChip® WT PLUS Reagent Kit.

growth_protocol: Mice were housed in a temperature-controlled room (22–24°C) with a 12h dark-light cycle and fed either a CSAA diet (control) or a CDAA supplemented with cholesterol, glucose and fructose. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use.

extract_protocol: RNeasy® Plus Kit and RNeasy® Lipid Tissue Kit respectively for primary hepatocytes and total livers according to the manufacturer’s instructions (Quiagen). Total RNA was checked for quantity and quality using the Agilent 2100 Bioanalyzer (Agilent Biotechnologies).

treatment_protocol: Hepatocytes were obtained after 2-step collagenase perfusion technique (Bantubungi K et al, Diabetes 2014). Caudal lobe from liver mice were obtained after cardiac perfusion with saline solution.

tag: tissuie

value: total liver

tag: strain

tag: gender

value: male

value: adult

value: WT

value: CDAA


title: MouseTL_CSAA_4

description: Transcriptomic TL CSAA

tag: age

value: CSAA


title: MouseTL_CDAA_3

description: Transcriptomic TL CDAA


title: MouseTL_CDAA_1

description: Transcriptomic TL CDAA


title: MouseTL_CDAA_2

description: Transcriptomic TL CDAA


title: MouseTL_CSAA_3

description: Transcriptomic TL CSAA


title: MouseTL_CSAA_2

description: Transcriptomic TL CSAA


title: MousePH_CDAA_1

description: Transcriptomic PH CDAA

value: primary hepatocytes


title: MouseTL_CSAA_1

description: Transcriptomic TL CSAA


title: MousePH_CDAA_3

description: Transcriptomic PH CDAA


title: NSD2_variant2

type: genomic

city: Setagaya

first: Tomoko

last: Kawai

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

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

data_processing:
R package minfi and ChAMP were used. We removed probes with detection P values of >0.01 in at least one sample and a bead count <3 in at least 5% of samples, and non-CpG targeting probes. We also filtered single-nucleotide polymorphism-related probes, multi-hit probes, probes located on either X or Y chromosome.
Normalized Average Beta: Background was corrected using the NOOB method in the minfi package, then NOOB-corrected data were normalised by BMIQ in the ChAMP package.

label: Cy5 and Cy3

source_name: disease peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood using QIAsymphony DNA Midi Kit (96) according to standard instructions

value: Female

value: 6 years

tag: disease state

value: Arachnoid cyst

tag: genetic variants inheritance

value: paternal inheritance

value: peripheral blood cells


title: MousePH_CSAA_3

description: Transcriptomic PH CSAA


title: Kabuki_2

value: 8 months

value: Kabuki Syndrome

value: de novo


title: Kabuki_1

value: 11 years


title: CHARGE

value: Male

value: 2 years

value: CHARGE Syndrome


title: del(4)(p16)_21

value: 5 years

value: WHS

value: NR


title: NSD2_Case1

value: 1 year

value: Developmental delay


title: Sotos_1

value: Female

value: Sotos Syndrome


title: NSD2_variant3

value: Hydrocephalus

value: maternal inheritance


title: Sotos_2

value: 5 months

value: peripheral blood cells


title: del(4)(p16)_20


title: del(4)(p16)_14


title: del(4)(p16)_16

value: 7 months


title: Day7_SatelliteCells_biol_rep4_RNA

first: Sundari

last: Chetty

address: 185 Cambridge Street

department: Harvard Medical School

institute: Massachusetts General Hospital, Harvard University

description: Day7_Sat_4_7_C9Y39ANXX.7.TAGGCATG_GCGTAAGA

data_processing:
RNA-seq: Paired-end RNA-seq samples from Illumina were aligned to the mm10 reference genome with the STAR aligner (STAR_2.5.0a)(Dobin et al. 2013) using default parameters.
RNA-seq: RSEM (Applied Research Applied Research Press 2015) quantification was applied to the aligned reads. All replicates were aligned and quantified separately -- there were two technical replicates for each timepoint/condition (WT vs KO).
Supplementary files format and content: RNA-seq: .tsv tab-separated text files containing the RSEM quantified expected count, FPKM, TPM at both the isoform and gene level. Rows indicate unique gene / transcript identifiers. Columns indicate unique replicates
ATAC-seq: The ATAC-Seq samples were analyzed with the ENCODE ATAC-seq processing pipeline( https://github.com/ENCODE-DCC/atac-seq-pipeline, version 1.1.1)(Lee et al. 2016). The cutadapt algorithm(Martin 2011) was used to trim adapters, and the Bowtie2(Langmead and Salzberg 2012) aligner was used to align the reads to an mm10 index. Duplicates were then removed from the aligned reads, and the MACS2(Langmead and Salzberg 2012; Zhang et al. 2008) peak caller was used to call peaks from the aligned ATAC-seq samples. The naive overlap peak set from all replicates for a given sample was used. Such peak sets from all samples were concatenated and merged using the bedtools merge command to produce a master peak set across all samples. The read counts for each sample at each peak were obtained by running bedtools coverage on the shifted de-deplicated tagAlign files generated by the pipeline.
Assembly: mm9
Supplementary files format and content: ATAC-seq: tagAlign (alignments to mm9)
Supplementary files format and content: ATAC-seq:  narrowPeak peak calls for top 500K peaks with p-value from MACS2 < 0.01, TN5-shifted
Supplementary files format and content: ATAC-seq:  narrowPeak peak calls for top 500K peaks with p-value from MACS2 < 0.01, TN5-shifted; with peaks derived from overlap of pseudo reps via ENCODE processing pipeline (“naive overlap”)
Supplementary files format and content: ATAC-seq: bigWigs, fold-change (from MACS2)
Supplementary files format and content: ATAC-seq: bigWigs, p-value (from MACS2)

source_name: Satellite Cells

extract_protocol:
RNA-seq: At least 10,000 FACS sorted muscle stem cells were deposited into Trizol (Thermo Fisher) and snap frozen immediately thereafter. After thawing, total RNA was isolated using the miRNeasy Micro Kit (Qiagen) as per the manufacturer’s instructions. The isolated RNA was quantitated and the integrity of the samples were verified with a Bioanalyzer (Agilent 2100).
RNA-seq:  Approximately 10ng of isolated total RNA from biological replicates was used to produce cDNA libraries using the SmartSeq4 protocol (Clontech), as per the manufacturer’s instructions. Individual libraries were pooled and sequenced using one lane of 76-bp paired-end reads on an Illumina High-Seq 2500 to an average depth of 50M reads per library.
ATAC-seq: At least 10,000 sorted muscle stem cells were sorted into 1.5 mL centrifuge tubes, spun down at 500xg for 5 min at 4˚C and the supernatant removed. After re-suspension in cold 1x PBS and centrifugation again at 500xg for 5 min at 4˚C, the cell pellets were re-suspended in 50 µL of cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-360), and centrifuged at 750xg for 15 min at 4˚C to pellet the nuclei. The nuclei were then re-suspended transposase reaction mix (12.5 µL 2x TD buffer, 1.25 µL TN5 transposase (Illumina) and 11.25 µL nuclease-free water), incubated at 37˚C for 35 min under mild agitation (300 rpm on a Thermo-Mixer C, Eppendorf). The transposed DNA fragments were purified (Qiagen MinElute PCR Purification Kit) as per manufacturer’s instructions, amplified using barcoded PCR primers and NEB Next High Fidelity 2x PCR Master Mix (New England Bio Labs) on a thermal cycler and purified again using double concentrated SPRI beads.
ATAC-seq: The concentration and size distribution of each was determined (Agilent 2100 Bioanalyzer), pooled and sequenced on a NextSeq (Illumina) using 76-bp paired-end reads to greater than 50M reads per library.

value: Satellite Cells

value: NEMO KO

tag: timepoint

value: Day 7


title: MousePH_CSAA_1

description: Transcriptomic PH CSAA

value: primary hepatocytes

value: male

value: adult

value: WT

value: CSAA


title: del(4)(p16)_17

value: Male

value: 1 month

value: WHS

value: NR


title: del(4)(p16)_18

value: Female

value: 5 years


title: Day7_SatelliteCells_biol_rep2_RNA

description: Day7_Sat_2_7_C9Y39ANXX.7.TCCTGAGC_GCGTAAGA


title: Day7_SatelliteCells_biol_rep1_RNA

description: Day7_Sat_1_7_C9Y39ANXX.7.AGGCAGAA_GCGTAAGA


title: Day7_SatelliteCells_biol_rep3_RNA

description: Day7_Sat_3_7_C9Y39ANXX.7.GGACTCCT_GCGTAAGA


title: del(4)(p16)_12

value: 1 year


title: MousePH_CDAA_2

description: Transcriptomic PH CDAA

value: CDAA


title: Day4_SatelliteCells_biol_rep3_RNA

description: Day4_Sat_3_7_C9Y39ANXX.7.TAAGGCGA_GCGTAAGA

value: Day 4


title: del(4)(p16)_8

value: 18 years

value: peripheral blood cells


title: ppk_delta_r1_DNA_gel

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

description: Gel extraction of high molecular weight BSB-associated region in delta ppk cells

data_processing:
The resulting gel-extracted reads were preprocessed using cutadapt to remove identifiable adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA in read 1, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT in read 2),
followed by Trimmomatic to remove low quality read ends (arguments: TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:14)
The resulting reads were aligned to the E. coli genome using bowtie2
The resulting reads were aligned to the E. coli genome using bowtie2 and then coverage quantified using bedtools genomecov
Assembly: E coli K12 U00096.3
Supplementary files format and content: *log10abund.bedgraph: normalized log10 ratio of extracted to input read densities at each location
Supplementary files format and content: *rzscore.bedgraph: robust z-scored version of the log10 ratios

organism: Escherichia coli K-12

source_name: cells

extract_protocol:
Gel-extracted DNA corresponding to the polyP dependent, Hfq-associated high molecular weight fraction on native gels was recovered by crushing the gel slice with a pipette tip, adding 200 microliters of PAGE elution buffer (0.5 M ammonium chloride, 0.03 M sodium acetate, 5 mM EDTA, 0.1% Tween20) and incubating for 6 hours at 37 C with shaking. At the end of the incubation, the sample was centrifuged 1 minute at 16,100xg at 4 C, and then an additional 100 microliters of PAGE elution buffer was added and vortexed, and the supernatant combined with the additional 200 microliter eluate. 600 microliters of ice cold ethanol were added to each sample, followed by overnight incubation at -80 C to precipitate the DNA.   After precipitation, the DNA was recovered by spinning 10 minutes at 16,100xg at 4 C, washing the pellet with 1 mL 95% ethanol, re-spinning, and then removing all ethanol from the pellet and allowing it to dry. The pellet was then resuspended in 200 microliters TE (pH 7.5). Half of the recovered material was treated with RNase A (final concentration 0.25 mg/mL) and purified using a Zymo DNA C&C kit according to the manufacturer’s instructions.
The recovered DNA was prepared for sequencing using a NEBNext Ultra 2 DNA sequencing preparation kit with UMI adapters

value: cells

tag: biological replicate

tag: sample type

value: condensate derived DNA

value: delta-ppk with hfq-mcherry

value: N-24 nitrogen starvation


title: Day4_SatelliteCells_biol_rep4_RNA

description: Day4_Sat_4_7_C9Y39ANXX.7.CGTACTAG_GCGTAAGA

value: Satellite Cells

value: NEMO KO


title: Day4_SatelliteCells_biol_rep2_RNA

description: Day4_Sat_2_7_C9Y39ANXX.7.TAGGCATG_AGAGTAGA


title: del(4)(p16)_13


title: NSD2_5

value: Male

value: 0 year

value: Hydrocephalus

value: homozygous


title: Wt_r1_DNA_gel

description: Gel extraction of high molecular weight BSB-associated region in WT cells

value: wild-type with hfq-mcherry


title: Wt_r2_DNA_gel


title: NSD2_Case2

value: 2 years

value: Developmental delay

value: de novo


title: NSD2_Case3

value: Female

value: 1 year


title: Arabidopsis thaliana 6d seedling sRNA-seq r2

city: Pullman

first: Sascha

last: Duttke

state: Washington

address: BLS 202, 100 Dairy Road

department: School of Molecular Biosciences

institute: Washington State University

description:
sRNA-seq; small RNA mapping in A.thaliana cells; Experiment MS344
A.thaliana-6dseedling-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
5’GRO-seq peaks were called using HOMER’s “findPeaks {5GRO_tagdirectory} -i {GRO_tagdirectory} -style tss -F 3 -P 1 -L 2 -LP 1 -size 150 -minDist 200 -ntagThreshold 10 > 5GRO_TSRs.txt”. Detailed explanation of each parameter can be found at http://homer.ucsd.edu/homer/ngs/tss/index.html.
Assembly: TAIR10, Phypa V3
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.

organism: Arabidopsis thaliana

source_name: 6d seedling

growth_protocol: For A. thaliana seedlings, seeds were sterilized using vapor-phase sterilization (seeds were exposed to 100 mL bleach + 3 mL concentrated HCl in a vacuum chamber for 3 hours), then approximately 20-40 seeds per plate were sown on 1x MS plates and stratified for 3 days at 4°C in the dark. Plates were transferred to growth room and grown for 6 days in long-day conditions (16 h light, 8 h dark). After 6 days, seedlings from each plate were harvested into Eppendorf tubes containing a metal ball bearing and immediately flash frozen in liquid nitrogen. Physcomitrium (Physcomitrella) patens (Gransden) was grown on plates with BCDA medium in a growth cabinet at 21°C under 16h light.

extract_protocol:
A. thaliana seedlings tissue was ground using the Qiagen TissueLyser II, at 1/30s frequency for 1.5 min twice. RNA was purified using the Zymo Direct-zol RNA MiniPrep kit.
csRNA-seq was performed as described in (S. H. Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-3 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by 1 hour incubation with Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen). Subsequently, RNAs were 5’dephosporylated through 90 minutes incubation in total with thermostable QuickCIP (NEB) in which the samples were briefly heated to 75°C and quickly chilled on ice at the 60 minutes mark. Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 11-14 cycles. Total RNA-Seq Library Preparation Strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Ribo-Zero Gold plant rRNA removal kit (Illumina, San Diego, CA). Samples were processed following the manufacturer’s instructions.

value: 6d seedling

tag: molecule type

value: short RNAs (20-65nt)


title: del(4)(p16)_9

value: 6 years

value: WHS

value: NR

value: peripheral blood cells


title: MousePH_CSAA_2

description: Transcriptomic PH CSAA

value: primary hepatocytes

value: male

value: adult

value: WT

value: CSAA


title: del(4)(p16)_15

value: 4 years


title: Day4_SatelliteCells_biol_rep1_RNA

description: Day4_Sat_1_7_C9Y39ANXX.7.GGACTCCT_AGAGTAGA

value: Satellite Cells

value: NEMO KO

value: Day 4


title: Day2_SatelliteCells_biol_rep3_RNA

description: Day2_Sat_3_6_C9Y39ANXX.6.AGGCAGAA_AGAGTAGA

value: Day 2


title: Arabidopsis thaliana 6d seedling csRNA-seq r2

description:
csRNA-seq; nascent TSS mapping in A.thaliana cells; Experiment MS336
A.thaliana-6dseedling-10.tss.txt


title: del(4)(p16)_10

value: Female

value: 3 years


title: Day2_SatelliteCells_biol_rep1_RNA

description: Day2_Sat_1_6_C9Y39ANXX.6.TAGGCATG_TATCCTCT


title: Arabidopsis thaliana 6d seedling csRNA-seq r1

description:
csRNA-seq; nascent TSS mapping in A.thaliana cells; Experiment MS335
A.thaliana-6dseedling-10.tss.txt

value: 6d seedling

value: short RNAs (20-65nt)


title: Day0_SatelliteCells_biol_rep4_RNA

description: Day0_Sat_4_6_C9Y39ANXX.6.GGACTCCT_TATCCTCT

value: Day 0


title: H2O2-treated rep2

city: Beijing

first: Huichun

last: Tong

address: NO. 3, Yihao Yuan, Beichen West Road, Chaoyang District, Beijing

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Gene expression profiles in H2O2-treated anaerobically grown S. oligofermentans

hyb_protocol: Each microarray chip slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies) according to the manufacturer’s instructions. After 17 h hybridization, slides were washed with Gene Expression Wash Buffer Kit,

scan_protocol: Microarray chips were scanned by Agilent Microarray Scanner with default settings.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies), and normalized using Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies).

organism: Streptococcus cristatus

source_name: S. oligofermentans, anaerobically grown, treated with H2O2, repeat 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies), and purified using RNeasy mini kit (QIAGEN).

growth_protocol: S. oligofermentans was anaerobically grown under 100% N2 in Brain Heart Infusion broth

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) following the manufacturer's recommendations. Qualified total RNA was further purified using RNeasy micro kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set (QIAGEN, GmBH, Germany)

treatment_protocol: One aliquot of S. oligofermentans was treated with 0.5 mM H2O2, leaving another aliquot untreated.


title: Day2_SatelliteCells_biol_rep2_RNA

city: Boston

description: Day2_Sat_2_6_C9Y39ANXX.6.CGTACTAG_AGAGTAGA


title: del(4)(p16)_19

value: WHS

value: NR


title: Day0_SatelliteCells_biol_rep3_RNA

description: Day0_Sat_3_6_C9Y39ANXX.6.TCCTGAGC_TATCCTCT


title: ppk_delta_r2_DNA_gel

value: cells

value: condensate derived DNA

value: delta-ppk with hfq-mcherry

value: N-24 nitrogen starvation


title: Day0_SatelliteCells_biol_rep2_RNA

description: Day0_Sat_2_6_C9Y39ANXX.6.CGTACTAG_TATCCTCT


title: non H2O2-treated rep2

description: Gene expression profiles in anaerobically grown S. oligofermentans

source_name: S. oligofermentans, anaerobically grown, repeat 2

value: non H2O2-treated


title: Day0_SatelliteCells_biol_rep1_RNA

description: Day0_Sat_1_6_C9Y39ANXX.6.TAAGGCGA_TATCCTCT


title: Arabidopsis thaliana 6d seedling sRNA-seq r1

description:
sRNA-seq; small RNA mapping in A.thaliana cells; Experiment MS343
A.thaliana-6dseedling-10.tss.txt


title: HS-3

city: Lanzhou

first: guiyan

last: zhao

address: Yingmen Village 1

institute: Gansu Agricultural University

data_processing:
sequenced using Illumina HiSeq6000 of Gene Denovo Biotechnology Co.
The short reads sequence alignment tool Bowtie2 (version 2.2.8) was used to map read sequences to the ribosomal RNA (rRNA) database, and the mapped reads were removed.
For each transcribed region, use StringTie software to calculate the FPKM (number of fragments per thousand base pairs of transcribed fragments per thousand base pairs) value to quantify its expression abundance and variation.
Assembly: Oncorhynchus mykiss Omyk_1.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

organism: Oncorhynchus mykiss

extract_protocol:
According to the manufacturer's protocol, total RNA from the liver of rainbow trout was extracted using the Trizol kit (Invitrogen, Carlsbad, California, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: Liver tissue

value: the experimental group is subjected to heat stress by treating the rainbow trout liver  in  24C for a duration of 8 h


title: HS-2


title: non H2O2-treated rep1

source_name: S. oligofermentans, anaerobically grown, repeat 1


title: Adult McSC 4

first: Melissa

last: Harris

state: AL

address: 1300 University Blvd, CH464

department: Biology

institute: University of Alabama at Birmingham

data_processing:
Bam files were assessed for low-quality reads and removed before converting to fastq file format using samtools (v1.9, RRID:SCR_014583) and Bam2fastq (v1.1.0) software.
Read quality was assessed using FastQC (v0.11.8, RRID:SCR_014583) and trimming was performed using Trimmomatic (v0.36, RRID:SCR_011848).
Reads with a Phred quality score of 30 were pairwise removed and the remaining paired reads were trimmed to an average length of 90 base pairs.
Reads were aligned to the Ensembl (RRID:SCR_002344) mouse mm10 reference genome with the STAR (v2.5.2, RRID:SCR_015899) aligner software using default parameters, and count tables were generated using the STAR genecounts feature and full Ensembl GTF annotation file.
Differential gene expression analysis was performed using DESeq2 (v1.22.2, RRID:SCR_015687) package in R using default settings.
Assembly: mm10
Supplementary files format and content: .tab files that contain raw counts after alignment using STAR -genecounts feature

source_name: body skin

growth_protocol: Animals used for RNA-Seq were housed at the animal facilities at NHGRI-NIH. C57BL/6J wildtype females (8-week-old) and pups (P0.5) were derived from in-house mating of C57BL/6J mice obtained from The Jackson Laboratory (JAX, JAX:000664, RRID: IMSR_JAX:000664). C57BL/6 wild-type female mice (24-month-old) were obtained through the NIA Aged Rodent Colony (Charles River Laboratories, RRID:SCR_007317) at 21 months old and allowed to age to 24 months within the same facility as the adult 8-week-old and P0.5 pups to which they were compared.

extract_protocol:
Cellular RNA was purified using the Directzol RNA Miniprep Kit (Zymo R2062). For RNA-Seq, RNA was treated with 0.8U/μl RNase inhibitor. RNA was quantified using a Qubit fluorometer. RNA quality was determined by Bioanalyzer and RNA samples with a RIN score >8.5 were used for sequencing.
Amplified cDNA was created from 20 ng total RNA using the Ovation RNA-Seq System V2 (Tecan Genomics). The cDNA was fragmented using a Covaris E210 before proceeding to library construction with 1000ng cDNA using TruSeq RNA Sample Prep Kit, version 2 (Illumina) using 10 PCR cycles. Libraries were pooled in equimolar ratio and sequenced together on a HiSeq 2500 with version 3 flow cells and sequencing reagents. At least 60 million 126-base read pairs were generated for each library. Data were processed using RTA 1.18.64 and CASAVA 1.8.2. RNA-Seq reads that passed the Illumina platform quality check were used for downstream analyses.

value: body skin

tag: developmental stage

value: quiescent melanocyte stem cells


title: CG-3

value: the control group involve placing rainbow trout liver  in  18C


title: H2O2-treated rep1

description: Gene expression profiles in H2O2 treated anaerobically grown S. oligofermentans

source_name: S. oligofermentans, anaerobically grown, treated with H2O2, repeat 1


title: HS-1


title: Adult McSC 3


title: Aged McSC 2


title: CG-2


title: CG-1


title: Aged McSC 1


title: del(4)(p16)_11

value: Female

value: 4 years

value: peripheral blood cells


title: Adult McSC 1


title: CRF518

city: Swansea

first: April

last: Rees

address: Room 203 ILS1, Singleton Park

institute: Swansea University

hyb_protocol: Lysed cell samples stored at -80°C were thawed on ice prior to hybridisation reactions. To create a master mix, reporter probes were diluted in 70 μl of hybridisation buffer. To set up the hybridisation reactions, 5 μl of each sample was added to 8 μl of master mix. Hybridisation reactions were then completed by adding 2 μl of Capture ProbeSet and incubation at 65°C for 20 h. Probe set-target RNA hybridisation solution is then further diluted to a final volume of 35 μl. 33 μl of the diluted hybridisation solution is loaded onto a SPRINT microfluidic cartridge, with an air bubble also inserted to the stop point.

scan_protocol: Detection and scanning were performed by the nCounter® SPRINT Profiler analysis system (Nanostring).

data_processing: Data analysis was performed using the advanced analysis package (2.0.134) within the nSolver© analysis software (Version 4.0, NanoString©), and differential expression p-value adjustment was done with Benjamini-Hochberg. Significant gene changes were determined to be p  ≤ 0.05 with a fold change of ≤ -0.5 or ≥0.5.

source_name: Human peripheral blood

label_protocol: Sample RNA is hybridised with target-specific capture and reporter probes in order to create a library of unique target-probe complexes. Each target is labelled with a specific molecular barcode, which can then be detected and counted using an automated fluorescence microscope

extract_protocol: Sample processing: 1 x 10^6 of monocytes were washed with 1 ml RPMI 1640/Glutamax and centrifuged at 8,000 x g for 4 mins. The cells were re-suspended with diluted RLT buffer (Qiagen, UK) (1/3 with RNase-free water; Invitrogen) to 10,000 cells / μl, and frozen at -80°C.

value: Peripheral blood

value: Monocytes

tag: participant group

value: Non-pregnant


title: Adult McSC 2


title: del(4)(p16)_7

value: 6 years

value: WHS

value: NR


title: Day2_SatelliteCells_biol_rep4_RNA

description: Day2_Sat_4_6_C9Y39ANXX.6.TCCTGAGC_AGAGTAGA

value: Satellite Cells

value: NEMO KO

value: Day 2


title: SI-Bone_marrow_recipient-4

city: Oberschleißheim

first: Caspar

last: Ohnmacht

address: Ingolstädter Landstraße 1

department: Institute for Allergy Research

institute: Helmholtz Munich

description:
BMR4
10X Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Small intestine lamina propria

extract_protocol:
Small intestine was extracted from mice and Peyer's patches were removed. Then intestine was opened longitudinally, washed in PBS and cut into 0.5-1 cm pieces. The pieces were then incubated in ice cold PBS with 30 mM EDTA for 30 min and thoroughly washed in PBS. Afterwards they were cut into smaller pieces and digested three times for 10 min, 20 min and 30 min in RPMI 1640 containing 25 mM HEPES, 0.5 mg/ml Collagenase D and 10 µg/ml DNaseI. Disintegrated supernatants were collected in RPMI1640 + 10% FCS in between digestion steps. Cells were then filtered to remove clumps and Percoll density gradient centrifugation (40%/80%) was performed to purify lymphocytes. Cells were stained with antibodies against CD45, CD3 and CD4 and before sorting 7AAD was added to label dead cells. They were then sorted for CD45+CD3+CD4+7AAD- using the FACS Aria III and collected in PBS with 0.04% BSA.
Prior to sorting cells were labeled with anti-CD45.1 TotalSeq-B0178 and anti-CD45.2 TotalSeqB0157 antibodies for feature barcoding. Library was prepared according to manufacturer's instructions (Chromium Next GEM Single Cell 3' Kit v3.1; 10X Genomics).

treatment_protocol: Rag1-/- mice were irradiated and then injected with 1x10^7 bone marrow cells from either WT CD45.1+ or Bcl3-/- CD45.2 mice in a 50:50 ratio. Mice were analyzed after 16 weeks.

value: Small intestine lamina propria

value: CD4+ T cells

value: transplant of mixed bone marrow from CD45.1+ WT and CD45.2+ Bcl3-/- mice


title: SI-Bone_marrow_recipient-3

description:
BMR3
10X Genomics


title: Melanoblast 3

value: body skin

value: melanoblats


title: SI-Bone_marrow_recipient-2

description:
BMR2
10X Genomics


title: SI-Bone_marrow_recipient-1

description:
BMR1
10X Genomics


title: CRF381


title: GH2O2_2

city: Nanjing

first: jun

address: 1 Weigang, Nanjing City, Jiangsu Province

institute: Nanjing Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
we use Cutadapt(v1.15) software to filter the sequencing data to get high quality sequence（Clean Data）forfurther analysis .
Thefiltered reads were mapping to the reference genome using HISAT2 v2.0.5
we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the originalexpression of the gene, and then used FPKM to standardize the expression.
Assembly: https://fungidb.org/fungidb/app/downloads/Current_Release/Poryzae70-15/
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Pyricularia oryzae

source_name: mycelium

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: mycelium

tag: cell line

value: Pyricularia oryzae

value: 5 mM H2O2 treatment


title: CRF072

tag: tissue

value: Peripheral blood


title: CAT1647

value: Monocytes

value: Pregnant


title: Physcomitrella patens plate culture total RNA-seq r1

description:
total RNA-seq (Ribo0), steady state transcriptome profiling in P.patens cells;
P.patens-Gransden-10.tss.txt

data_processing:
csRNA-seq (small capped RNAs, ~20-60 nt) and sRNA-seq reads (“input”) were trimmed of their adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20" none -f {csRNA_fastq_path}/*fastq.gz”)(Heinz et al. 2010). Reads were aligned to the appropriate genome using Hisat2 version 2.2.1 (Kim et. al. 2019) with parameters “hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_genome_index} -U {path_rimmed_csRNA or sRNA} -S {output_sam} 2> {mapping_stats}”. Hisat2 indices were then created for each genome used ("hisat2-build -p 40 genome.dna.toplevel.fa {Hisat2_indexfolder}") with exception for barely which required the addition of "--large-index" due to genome size. Tag directory folders were then created using HOMER makeTagDirectories ("makeTagDirectories {outputName} -omitSN -checkGC -fragLength 150 -single")(Heinz et. al. 2010). Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. This consolidates the aligned read information into a read/chromosome format along with other important alignment information. Peaks were called and annotated using HOMER ("findcsRNATSS.pl {csRNA} -o {output} -i {sRNA} -genome hg38 -size 150 -ntagThreshold 10") (Duttke et al. 2019) and annotatePeaks.pl ("annotatePeaks.pl {tss/tsr.txt} hg38 -strand + -fragLength 1 -rlog -d {listOfTagDirs} > {output}") (Heinz et. al. 2010) respectively (additional details available in the manuscript).
Transcription start sites (TSSs) and Transcription start regions (TSRs) were determined in this study. TSRs  were called using findcsRNATSS.pl (detailed above) while TSSs were called using getTSSfromReads.pl ("getTSSfromReads.pl -d {csRNA_tagdir} -dinput {sRNA_tagdir} -min 7 > {output_file}") (Heinz et. al. 2010). To ensure high quality TSSs, at least 7 per 10^7 aligned reads were required and TSS were required to be within called TSR regions.
Paired end total ribosomal RNA-depeleted RNA-seq libraries were trimmed using skewer (“time -p skewer -m mp {read1} {read2} -t 40 -o {trimmed_fastq_output}”) (Jiang et al. 2014) and aligned using Hisat2 (Kim et al. 2019) to ensure all data were processed as similar as possible (“hisat2 -p 30 --rna-strandness RF --dta -x {hisat2_index} -1 {trimmed_RNAseq_R1} -2 {trimmed_RNAseq_R2} -S {output_sam} 2> {mapping_file}”). In this manuscript, total RNA-seq was exclusively used to determine RNA-stability as described in the csRNA-seq analysis.
Assembly: TAIR10, Phypa V3
Supplementary files format and content: bed files: Locations indicate TSS positions. TSS.txt files: text files containing tab delimited  information about found transcription start site culsters (TSRs). Motif file containing new line delimited motifs. Motif files: files containing motifs used with a ‘>’ indicating motif information followed by rows with nucleotide probability.

organism: Physcomitrium patens

source_name: plate culture

growth_protocol: Physcomitrium (Physcomitrella) patens (Gransden) was grown on plates with BCDA medium in a growth cabinet at 21°C under 16h light.

value: plate culture


title: Melanoblast 1

organism: Mus musculus


title: Melanoblast 2


title: CAT1645


title: del(4)(p16)_6

value: Female

value: 18 years

value: WHS

value: peripheral blood cells


title: CAT1646


title: NSD2_variant1

value: Marfan syndrome like

value: maternal inheritance


title: GH2O2_1

tag: genotype


title: SI-WT-3

description:
GEX3
10X Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

extract_protocol:
Small intestine was extracted from mice and Peyer's patches were removed. Then intestine was opened longitudinally, washed in PBS and cut into 0.5-1 cm pieces. The pieces were then incubated in ice cold PBS with 30 mM EDTA for 30 min and thoroughly washed in PBS. Afterwards they were cut into smaller pieces and digested three times for 10 min, 20 min and 30 min in RPMI 1640 containing 25 mM HEPES, 0.5 mg/ml Collagenase D and 10 µg/ml DNaseI. Disintegrated supernatants were collected in RPMI1640 + 10% FCS in between digestion steps. Cells were then filtered to remove clumps and Percoll density gradient centrifugation (40%/80%) was performed to purify lymphocytes. Cells were stained with antibodies against CD45, CD3 and CD4 and before sorting 7AAD was added to label dead cells. They were then sorted for CD45+CD3+CD4+7AAD- using the FACS Aria III and collected in PBS with 0.04% BSA.
Library was prepared according to manufacturer's instructions (Chromium Single Cell 5' Library; 10X Genomics).

value: Small intestine lamina propria

tag: cell type

value: CD4+ T cells

value: Wildtype


title: SI-WT-2

description:
GEX2
10X Genomics


title: GCK2

tag: treatment

value: CK


title: del(4)(p16)_5

value: 5 years

value: NR


title: GCK1

value: mycelium

value: Pyricularia oryzae


title: SI-WT-1

description:
GEX1
10X Genomics