title: RAD21 ChIP-M of Del(CBS1) stembryos at 96h, rep1

data_processing:
All scripts are available on https://github.com/lldelisle/scriptsForRekaikEtAl2022
Fastqs of the 3 replicates of wt_144h_pSer2PolII were concatenated before any processing.
Adapter sequences were trimmed from reads using cutadapt (Martin et al 2011) version 1.16 (-a 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC' -A 'GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT' for ChIP and -a 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' -A 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' for ChIPmentation).
Trimmed reads were mapped on mm10 genome or the mutant genome Ins(2xCBS-d4d8) for the corresponding  mutant CTCF ChIPmentation) using bowtie2 version 2.3.4.1 (Langmead et al. 2012).
Only aligments with proper pairs and mapping quality above 30 were kept using samtools 1.8.
Peaks and coverage were obtained with macs2 version 2.1.1.20160309 (--format BAMPE --gsize 1870000000 --call-summits --bdg).
In order to better compare ChIP, ChIP for the same protein with a time-course were normalized together using a custom python script (available in the github repository). Similarly, this normalization was used when mutant and control were performed in parallel (see supplementary table).
For H3K27ac and H3K27me3, in figure 7B and S10A, in order to reduce the impact of variations in gastruloid growth speed, the profile of mutant and corresponding wild-type were corrected using the time-course experiment and the profile around the HoxA cluster as a guide (see github repository for more details).
Assembly: mm10 or Ins(2xCBS-d4d8) for the sample Ins(2xCBS-d4d8)_144h_CTCF
Supplementary files format and content: *.narrowPeak.gz: narrowPeak from macs2
Supplementary files format and content: *.bigwig: macs2 coverage
Supplementary files format and content: *_Normalized.bigwig: macs2 coverage normalized between experiments for time-course or mutant and corresponding controls (see supplementary table)
Supplementary files format and content: *_Normalized_HCN_*h.bedgraph.gz: macs2 normalized coverage on the Hox clusters corrected for variation in gastroloid growth speeds using the profile around HoxA cluster and time-course as a guide

source_name: stembryo

extract_protocol:
Collected stembryos were pooled in a 15 ml falcon tube, washed with PBS and resuspended in 1 ml PBS containing 1% formaldehyde for fixation during 10 min at room temperature. The crosslink reaction was stopped by adding a glycine solution to a final concentration of 0.125 M. Fixed stembryos were pelleted and stored at -80°C until further use.
ChIP and ChIP-M experiments were performed according to the protocol described in (Rodriguez-Carballo et al., 2017) and (Darbellay et al., 2019), and adapted for stembryos samples. Samples were resuspended in a sonication buffer (Tris HCl pH=8.0 50 mM; EDTA 10 mM; SDS 0.25% and protease inhibitors) and sonicated in a Covaris E220 device for 14 min (duty cycle 2%, peak incident power 105 W) to obtain an average chromatin fragment size of 300-500 bp. A dilution buffer (HEPES pH=7.3 20 mM; EDTA 1 mM; NP40 0.1%; NaCl 150 mM and protease inhibitors) was added to the sonicated chromatin and incubated with the antibody-bead complex (Pierce Protein A/G Magnetic Beads, Thermo Scientific) overnight at 4°C. Sequential washes were then performed twice with RIPA buffer (Tris HCl pH=8.0 10 mM; EDTA 1 mM; Sodium Deoxycholate 0.1% TritonX-100 1%; NaCl 140 mM and protease inhibitors), RIPA High salt buffer (Tris HCl pH=8.0 10 mM; EDTA 1 mM; Sodium Deoxycholate 0.1% TritonX-100 1%; NaCl 500 mM and protease inhibitors), LiCl buffer (Tris HCl pH=8.0 10 mM; EDTA 1 mM; LiCl 250 mM; Sodium Deoxycholate 0.5%; NP40 0.5% and protease inhibitors) and Tris HCl buffer (pH=8.0 10mM and protease inhibitors). For ChIP experiments (H3K27ac (ab4729, Abcam), H3K27me3 (39155, Active Motif), CDX2 (sc-393572, Santa Cruz) and PolII-Ser2p (04-1571, Millipore)), DNA fragments were incubated in the elution buffer (Tris HCl pH=8.0 10 mM; EDTA 5 mM; NaCl 300 mM and SDS 0.1%) containing proteinase K and purified using the Qiagen MiniElute kit. A phosphatase inhibitor (PhosStop, Roche) was used during PolII-Ser2p ChIP incubation and beads wash. The DNA library was produced using TruSeq adapters and amplified with the Kapa HiFi library kit (Roche) using a number of cycles determined by qPCR. For ChIP-M samples (CTCF (61311, Active Motif), PolII (ab817, Abcam), RAD21 (ab992, Abcam) and NIPBL (A301-779A, Bethyl Laboratories)), DNA fragments bound to the antibody-bead complex were tegmented using the Nextera Tegmentation kit. Beads were resuspended in the tegmentation buffer and incubated at 37° for 2 min with 1 µl of the Tn5 transposase. Fragment were then eluted and purified as described previously, and amplified using Nextera primers. Final DNA libraries were purified and size selected using AMPure XP magnetic beads (Beckman Coulter), and a fragment analysis was performed before sequencing

value: stembryo

tag: cell line

value: mES cells

tag: stage (in_hours_after_aggregation)

tag: chip antibody

value: RAD21 (ab992, Abcam)


title: Injured Old H5

status: Public on Apr 28 2023

type: SRA

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

country: USA

institute: Washington University in Saint Louis

description: RNA was isolated from 3 mice

library_source: transcriptomic single cell

data_processing:
Demultiplexing with custom Python and perl script
Aligned to the Ensembl release 76 top-level assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Assembly: mm10
Supplementary files format and content: raw gene counts for all cells

molecule: total RNA

organism: Mus musculus

source_name: Spinal cord meninges

extract_protocol:
For the contusion injury, mice were anesthetized with ketamine (100 mg/kg)-xylazine (10 mg/kg) mixture. A 15-mm midline skin incision was made, and the connective tissue and muscles were bluntly dissected to expose T6-T13. Laminectomy was performed at T9 to expose the dorsal spinal cord, and the vertebral column was stabilized with angled clamps attached to the T7 and T12 transverse processes. The contusion injury was delivered using an Infinite Horizon Impactor (IH-0400 Impactor) with a force of 90 dynes. After injury, the muscles and skin were sutured separately. Mice were humanely euthanized with an intraperitoneal injection of a lethal dose of Euthasol® (10% v/v), followed by transcardiac perfusion of PBS with 5 U/mL of Heparin. Vertebral columns were obtained. The ventral bone of the vertebrae was cut laterally and was removed to expose the spinal cord. Nervous tissue was carefully dissected from the bone using fine forceps to release the dorsal root ganglia surrounded by the meninges. The meninges was cut along the ventral side and peeled from the spinal cord. Spinal cord meninges was enzymatically digested in RPMI containing 1 mg/mL collagenase VIII, 0.5 mg/mL DNase I, and 2% FBS for 30 minutes at 37°C with shaking. Samples were passed through a 70 µm filter to obtain single-cell suspensions, washed with FACS buffer, and pelleted at 380 xg for 5 minutes. Cells were resuspended in FACS buffer with 1:100 CD16/32 Fc block. They were stained with CD31, CD45, Podoplanin and Lyve1, washed, and resuspended in DAPI-containing FACS buffer. Single meningeal lymphatic endothelial cells were sorted as Live (DAPI-) CD45- CD31+ PDPN+ Lyve1+ cells using a FACS Aria II. Individual cells were sorted into 96-well plates containing 2 µL of 10X RNA lysis buffer (Takara) and 5% RNAse out (Takara) and rapidly frozen over dry ice.
Library preparation was performed with 2 µL of single cell lysates arrayed in 96-well PCR plates. ds-cDNA was prepared using a protocol adapted from the Takara-Clontech SMARTer methods. cDNA was blunt ended, had an A base added to the 3’ ends, and had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified using a standard Illumina i7 primer to introduce an index sequence and FACSseq Lib PCR 1.0 specific to fragments containing the cell barcode added during cDNA synthesis. Fragments were sequenced on an Illumina NovaSeq.

tag: tissue

value: Spinal cord meninges

tag: age

value: 24 months

tag: cell type

value: Lymphatic endothelial cells

tag: genotype

tag: Sex

value: female

tag: sample group

value: Injured


title: Injured Old H6

description: RNA was isolated from 3 mice


title: IT5

city: Rotterdam

first: Andre

last: Boonstra

state: Zuid-Holland

address: Wytemaweg 80

department: Gastroenterology & Hepatology

country: Netherlands

institute: Erasmus MC

library_source: transcriptomic

data_processing:
Raw paired-end reads were aligned to human reference genome hg38 downloaded from the USCS Genome Bioinformatics site using the STAR (v.2.7.3a).
Picard tools were employed to detect at least 10 million reads in protein coding mRNA regions for downstream analysis.
Quantification of gene expression was calculated using featureCounts (v.1.4.6-p1), converted to reads per kilobase per million mapped reads (RPKM) using the R package edgeR.
Subsequently, scores were calculated for gene sets from MSigDB v7 using the R GSVA package.
Gene counts per sample were used to perform differentialgene expression analysisbetween groups using the DESeq2 package (v.1.30.1).
Assembly: human reference genome hg38
Supplementary files format and content: Excel file RPKM

organism: Homo sapiens

source_name: Liver

extract_protocol:
Eight 10 µm-thick core needle liver biopsies were sectioned, deparaffinized, and total RNA was isolated using the RNeasy FFPE Kit (Qiagen, Germany) following the manufacturer’s instructions. rRNA was depleted using the Illumina Ribo-Zero rRNA Depletion kit (Illumina, USA) following the manufacturer’s instructions, and fragmented into approximately 300 basepairs (bp)
cDNA libraries for each sample were prepared using Illumina TrueSeq Total Gold
RNA-seq using 100 bp paired-end reads on Illumina HiSeq platform

tag: disease state

value: chronic HBV, phase IT

value: Liver

tag: treatment


title: wt_144h_RAD21_rep3

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

library_source: genomic

molecule: genomic DNA

value: wt


title: IT3


title: Injured Old H3

description: RNA was isolated from 3 mice


title: scRNA-seq of the posterior part of wt stembryos at 120h, rep1

data_processing:
All scripts are available on https://github.com/lldelisle/scriptsForRekaikEtAl2022
The cellranger pipeline version 6.0 (10x Genomics) was used with the default parameters on each fastq pair of scRNAseq datasets to perform the alignment, applying filtering and count barcodes and UMIs. Alignment was performed against the mouse reference genome mm10 and a modified gtf file based on Ensembl version 98 (https://doi.org/10.5281/zenodo.4456701). Each gene-cell count matrix was then analyzed using Seurat version 4.0.2 (Stuart et al. 2019). A Seurat object was generated by filtering out barcodes with less than 200 identified gene and genes identified in less than 3 cells. Then a further filtering was applied to remove low quality cells as well as doublets. For each dataset, the mean RNA count was used and cells with either less than 40% of the mean? or more than 2.5-fold the mean were remove. In addition, cells with more than 8% or less than 0.05% mitochondrial counts were removed. Each dataset was then normalized using the NormalizeData command, the 3000 most variable features were identified, and cell cycle was scored (using the 2019 updated gene list from Seurat). Then, all individual datasets were merged into a single Seurat object. The merged dataset was then normalized, the 3000 most variable features were identified. Then data scaling was performed using the ScaleData command using the percentage of mitochondrial count and cell cycle score.
Assembly: mm10
Supplementary files format and content: combined.96h.120h.rds: final R object containing filtered cells with expressions, clustering, projection etc. savec with saveRDS
Supplementary files format and content: filtered_feature_bc_matrix.tar: tar archive with output of cellranger (raw counts, gene names and cell names)
Supplementary files format and content: metadata.csv.gz: comma separated table containing metadata for each cell (clustering, sample of origin etc)
Supplementary files format and content: raw_counts.csv.gz: comma separated table contaiing the raw counts (genes as row and cells as columns)

source_name: stembryo (posterior part)

extract_protocol:
48 to 96 gastruloids were collected 96h or 120h after aggregation and washed twice in 1ml of PBS. Gastruloids were dissociated in 100ul of Stempro Accutase© for 5 minutes at 37°C, full dissociation was ensured by mechanical dissociation (pipetting) and verified to ensure absence of doublet cells. Then gastruloid cells were washed twice in 500ul PBS, and resuspended in an adequate volume of PBS 0.04%BSA at 106 cells/ml. All centrifugation steps were done for 5 minutes at 350G in DNA low binding Eppendorf tubes. Single cell suspensions were filtered using Flowmi Cell Strainer 40um and then were subjected to single cell RNAseq using the 10x genomics platform (V3, and V3.1 chemistry) following manufacturer’s recommendation.
cDNA preparations were performed according to 10x Genomics recommendations and was amplified for 10 to 12 cycles. And sequenced on a Hiseq 4000 with the cbot2 chemistry. At least 2 replicates were performed for each time points. In addition, a third 120h timepoint was generated by dissection in two portions to separate the anterior and posterior halves and each portion was analyzed separately by single cell RNAseq.

value: stembryo (posterior part)


title: IT4


title: Injured Old H4

description: RNA was isolated from 3 mice


title: wt_132h_RAD21_rep2


title: wt_108h_RAD21_rep2


title: Injured Young A2

description: RNA was isolated from 5 mice

value: 3 months


title: scRNA-seq of the anterior part of wt stembryos at 120h, rep1

source_name: stembryo (anterior part)

value: stembryo (anterior part)


title: IT2


title: Injured Old G12

description: RNA was isolated from 3 mice


title: IT7


title: Injured Old H10

description: RNA was isolated from 3 mice


title: RAD21 ChIP-M of Del(CBS1) stembryos at 96h, rep2


title: IT13


title: wt_96h_RAD21_rep3


title: Injured Old G11

description: RNA was isolated from 3 mice


title: Injured Old G10

description: RNA was isolated from 3 mice


title: IT1


title: wt_84h_RAD21_rep2


title: HC9

value: HC


title: wt_72h_RAD21_rep2


title: Injured Old G9

description: RNA was isolated from 3 mice


title: Injured Old G8

description: RNA was isolated from 3 mice


title: Injured Old G7

description: RNA was isolated from 3 mice


title: HC8


title: Injured Old G6

description: RNA was isolated from 3 mice


title: Injured Old H2

description: RNA was isolated from 3 mice


title: Injured Old G5

description: RNA was isolated from 3 mice


title: HC7


title: Injured Old G4

description: RNA was isolated from 3 mice


title: Injured Old H1

description: RNA was isolated from 3 mice


title: HC6


title: Injured Old G3

description: RNA was isolated from 3 mice


title: Injured Old G2

description: RNA was isolated from 3 mice


title: wt_48h_RAD21_rep1


title: Injured Old F12

description: RNA was isolated from 3 mice


title: HC5


title: Injured Old G1

description: RNA was isolated from 3 mice


title: H3K27ac ChIP of Del(CBS1-2) stembryos at 120h, rep1

value: H3K27ac (ab4729, Abcam)


title: H3K27ac ChIP of Del(CBS1-2) stembryos at 96h, rep2


title: Injured Old F10

description: RNA was isolated from 3 mice


title: HC4


title: H3K27ac ChIP of Del(CBS1-2) stembryos at 120h, rep2


title: Injured Old F8

description: RNA was isolated from 3 mice


title: HC3


title: Injured Old F11

description: RNA was isolated from 3 mice


title: Injured Old F9

description: RNA was isolated from 3 mice


title: H3K27ac ChIP of Del(CBS1-2) stembryos at 96h, rep1


title: CDX2 ChIP of wt stembryos at 120h

value: CDX2 (sc-393572, Santa Cruz)


title: Injured Old F7

description: RNA was isolated from 3 mice


title: HC2


title: Injured Old F6

description: RNA was isolated from 3 mice


title: Injured Old F5

description: RNA was isolated from 3 mice


title: Injured Old F4

description: RNA was isolated from 3 mice


title: CDX2 ChIP of wt stembryos at 96h

value: stembryo


title: Injured Old F3

description: RNA was isolated from 3 mice


title: HC1


title: CDX2 ChIP of wt stembryos at 72h

value: mES cells


title: Injured Old F2

description: RNA was isolated from 3 mice


title: CHi-C of wt stembryos at 144h, rep3

data_processing:
library strategy: Capture Hi-C
All scripts are available on https://github.com/lldelisle/scriptsForRekaikEtAl2022
TruSeq adapters were removed with cutadapt (Martin et al 2011) version 1.16 (-a 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' -A 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT').
Trimmed reads were processed with HiCUP version 0.6.1 (doi: 10.12688/f1000research.7334.1) with default paramters on mm10 or on the corresponding mutant genome.
The output BAM was converted to Juicebox format thanks to a custom python script available in  https://testtoolshed.g2.bx.psu.edu/repository/download?repository_id=be5040251cd4afb7&changeset_revision=44365a4feb3b&file_type=gz
Only pairs with both mates falling into the capture region (mm10:chr2:72402000-77000000) and with both mates with quality above 30 were kept.
Filtered pairs were loaded into 2kb and 5kb matrices with cooler version 0.7.4 (Abdennur, N., and Mirny, L. (2019), https://doi.org/10.1093/bioinformatics/btz540).
The matrices were balanced with cooler balance (--cis-only).
For the mutant Del(subTAD1), the balancing was done with the option --ignore-diags 5 instead of --ignore-diags 2 to discard the bias due to the presence of a BAC containing the region (mm10:chr2:74747769-74913171).
Assembly: mm10 for wt samples and Del(CBS*) samples and mutant genomes for Del(d1-d4) and Del(sub-TAD1)
Supplementary files format and content: *_validPairs_*.txt.gz: all valid pairs from HiCUP in juicebox format (<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse)   pos = middle of the fragment)
Supplementary files format and content: *_*kb_Balanced_*.cool: balanced matrix at 2 or 5kb-bins only in the captured region

extract_protocol:
Collected stembryos were pooled and fixed for 10 min in 1% formaldehyde at room temperature and stored at -80°C until further use.
Lysis was performed with TissueLyser II and metallic beads for 30 sec at 30 hertz before incubation at 4° for 30 min. The rest of the protocol for the capture Hi-C library generation is described in (Bolt et al., 2021). The costume SureSelectXT RNA probe used for DNA capture covers the region chr2:72240000-76840000 (mm9).


title: Injured Old F1

description: RNA was isolated from 3 mice


title: CHi-C of wt stembryos at 144h, rep2


title: Injured Old E12

description: RNA was isolated from 3 mice


title: Injured Old E11

description: RNA was isolated from 3 mice


title: 2515882_DOE16_22

city: Memphis

first: Jonanthan

last: Yen

state: TN

address: 262 Danny Thomas Pl

department: Hematology

institute: St. Jude Children's Research Hospital

description: RNA-seq

data_processing:
Reads were mapped to hg19 using STAR --twopassMode Basic
Bam files were processed using https://github.com/BioinfoUNIBA/REDItools
gene expression was quantified using kallisto based on cDNA ensembl v94
Assembly: hg19
Supplementary files format and content: tpm

growth_protocol: Healthy donor CD34+ HSPCs were cultured at a density of 0.5-1.0x10e6/mL in X-VIVO 10 (Lonza, BEBP02-055Q) medium supplemented with 100 ng/µL recombinant human SCF (R&D systems, 255-SC/CF), 100 ng/µL recombinant human TPO (R&D systems, 288-TP/CF), and 100 ng/µL recombinant Flt-3 ligand (R&D systems, 308-FK/CF).

extract_protocol:
One million cells from each treatment condition were collected and the RNA was extracted using a Qiagen RNeasy Plus Mini kit (# 74136).
Libraries were prepared using standard reagents from New England BioLabs for Illumina sequencing

tag: donor

tag: time

value: day 6_EP ctrl


title: 2515884_DOE16_24

description: RNA-seq

value: day 6_ABE8e


title: 2515883_DOE16_23

description: RNA-seq

value: day 6_ABE7.10


title: CHi-C of wt stembryos at 96h, rep3


title: 2515881_DOE16_21

description: RNA-seq

value: day 6_UT


title: CHi-C of wt stembryos at 96h, rep2


title: Injured Old E7

description: RNA was isolated from 3 mice

value: Spinal cord meninges

value: 24 months

value: Lymphatic endothelial cells

value: female


title: Injured Old E6

description: RNA was isolated from 3 mice

value: Injured


title: Injured Old E9

description: RNA was isolated from 3 mice


title: Injured Old E10

description: RNA was isolated from 3 mice


title: Injured Old E8

description: RNA was isolated from 3 mice


title: Injured Old E5

description: RNA was isolated from 3 mice


title: 2515879_DOE16_19

description: RNA-seq


title: CHi-C of wt stembryos at 48h, rep3

value: wt


title: CHi-C of wt stembryos at 48h, rep2


title: Injured Old E3

description: RNA was isolated from 3 mice


title: Injured Old E4

description: RNA was isolated from 3 mice


title: 2515878_DOE16_18

description: RNA-seq


title: Injured Old E1

description: RNA was isolated from 3 mice


title: Injured Old D12

description: RNA was isolated from 3 mice


title: 2515877_DOE16_17

description: RNA-seq


title: Injured Old D11

description: RNA was isolated from 3 mice


title: 2515876_DOE16_16

description: RNA-seq


title: RNA-seq of Ins(2xCBS-d4d8) stembryos at 120h, rep1

data_processing:
All scripts are available on https://github.com/lldelisle/scriptsForRekaikEtAl2022
Adapter sequences were trimmed from reads using cutadapt (Martin et al 2011) version 1.16 (-a 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC' -A 'GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT').
Trimmed reads were aligned on mm10 with STAR version 2.7.7a (Dobin et al. 2013) with ENCODE options using a custom gtf based on Ensembl version 102 (https://doi.org/10.5281/zenodo.4596490).
Only uniquely mapped reads (tag NH:i:1) were kept using bamFilter version 2.4.1 (Barnett et al. 2011).
FPKM values were computed using cufflinks version 2.2.1 (Trapnell et al. 2010; Roberts et al. 2011) with default parameters.
Assembly: mm10
Supplementary files format and content: *_FPKM.txt.gz: output of cufflinks with FPKM values per gene
Supplementary files format and content: all_FPKM.txt.gz: all FPKM values combined into a single table, one raw per gene_id and one column per sample

extract_protocol:
Stembryos for each condition were collected and pooled in a 2 ml Eppendorf tube. After centrifugation and medium removal, pelleted stembryos were stored at -80°C until RNA extraction.
RNeasy Plus Micro kit (Qiagen) with on-column DNase digestion was used for RNA extraction following the manufacturer’s instructions.
RNA-seq library preparation with Poly-A selection was performed with 1 µg of purified RNA using the TruSeq Stranded mRNA kit from Illumina and following the manufacturer’s protocol. Library quality was assessed with Fragment analyzer.


title: RNA-seq of Ins(2xCBS-d4d8) stembryos at 120h, rep2


title: RNA-seq of Ins(2xCBS-d4d8) stembryos at 96h, rep2


title: 2515880_DOE16_20

description: RNA-seq


title: Injured Old D7

description: RNA was isolated from 3 mice


title: 2515875_DOE16_15

description: RNA-seq


title: Injured Old D9

description: RNA was isolated from 3 mice


title: 2515874_DOE16_14

description: RNA-seq


title: RNA-seq of Ins(2xCBS-d4d8) stembryos at 96h, rep1


title: Injured Old D8

description: RNA was isolated from 3 mice


title: Injured Old D6

description: RNA was isolated from 3 mice


title: Injured Old D5

description: RNA was isolated from 3 mice


title: RNA-seq of Del(sub-TAD1) stembryos at 120h, rep1


title: Injured Old D4

description: RNA was isolated from 3 mice


title: 2515873_DOE16_13

description: RNA-seq


title: RNA-seq of Del(sub-TAD1) stembryos at 120h, rep2


title: Injured Old D2

description: RNA was isolated from 3 mice


title: RNA-seq of Del(sub-TAD1) stembryos at 96h, rep3


title: Injured Old D3

description: RNA was isolated from 3 mice


title: Hudep2_rep1_S2

description: MicroC

data_processing:
Data was processed using the MicroC pipeline: https://github.com/jojdavies/Micro-Capture-C
Assembly: hg19
Supplementary files format and content: bigwiggle
Library strategy: Micro-Capture-C

growth_protocol: Hemizygous HUDEP-2 cells were cultured at a density of 0.3-0.5x10e6/mL in StemSpan serum-free expansion medium (SFEM; Stemcell Technologies) supplemented with 1 μM dexamethasone, 1 μg/mL doxycycline, 50 ng/ml human SCF (R&D Systems), 3 U/mL EPO (Amgen), and 1% penicillin/streptomycin.

extract_protocol:
1–2 × 107 cells were fixed for 10 min at room temperature with formaldehyde (Sigma # 252549)  at a final concentration of 2% and quenched with 1 M glycine (Sigma # G7126). After centrifugation, the cell pellet was washed and reconstituted in 1 mL of PBS and permeabilized with 0.005% digitonin (Sigma # D141) for 5–10 min. Permeabilized cells were collected by centrifugation at 500 × g for 5 min and resuspended in low-calcium micrococcal nuclease (MNase) buffer (50 mM Tris-HCl pH 7.5, 1 mM CaCl2). Cells were digested with MNase (NEB # M0247) (7.5 to 50 Kunitz Units) in a reaction volume of 800 µL containing 4 × 106 cells at 37 °C for 1 h on an Eppendorf Thermomixer at 550 rpm. The reaction was quenched by adding ethylene glycol-bis(2-aminoethylether)-N,N,N′,N′-tetra acetic acid (EGTA) (bioWORLD # 405200085) to a final concentration of 5 mM. A 200 µL aliquot was removed as a control to test the digestion efficiency. The reaction mixture was then centrifuged for 5 min at 300 × g, and the digestion buffer was discarded. The cells were resuspended in DNA ligase buffer (Thermo Fisher # EL0013) with 10 mM dNTPs (NEB # N0447L), 5 mM EGTA, 200 U/mL T4 polynucleotide kinase PNK (NEB # M0201L), 100 U/mL DNA polymerase I large (Klenow) fragment (NEB # M0210L), and 300 U/mL T4 DNA ligase (Thermo Fisher # EL0013). The reaction mixture was shaken horizontally on an Eppendorf Thermomixer at 550 rpm (shaking for 15 s then pausing for 30 s) for 2 h at 37 °C then for 8 h at 20 °C. The chromatin was reverse crosslinked with proteinase K at 65 °C (for >4 h), and the DNA was extracted using a Qiagen DNeasy Kit (# 69506). Next, 1–10 μg of DNA from the MNase 3C libraries was sonicated with a Covaris E220 Focused Ultrasonicator (Duty cycle, 10%; intensity, 5; cells per burst, 200; time, 200–300 s).
Libraries were prepared using standard reagents from New England BioLabs for Illumina sequencing

tag: protocol

value: MicroC


title: Injured Old E2

description: RNA was isolated from 3 mice


title: Hudep2_rep2_S5

description: MicroC


title: Injured Old D1

description: RNA was isolated from 3 mice


title: Injured Old C12

description: RNA was isolated from 3 mice


title: RNA-seq of Del(sub-TAD1) stembryos at 96h, rep2


title: Injured Old C11

description: RNA was isolated from 3 mice


title: Hudep1_rep2_S4

description: MicroC


title: Injured Old D10

description: RNA was isolated from 3 mice


title: Hudep1_rep1_S1

description: MicroC


title: Injured Old C10

description: RNA was isolated from 3 mice


title: Injured Old C9

description: RNA was isolated from 3 mice


title: RNA-seq of Del(sub-TAD1) stembryos at 96h, rep1


title: RNA-seq of Del(d1-d4) stembryos at 120h, rep2


title: Injured Old C7

description: RNA was isolated from 3 mice


title: Injured Old C6

description: RNA was isolated from 3 mice


title: Injured Old C4

description: RNA was isolated from 3 mice


title: Hudep2_175_rep2_S6

description: MicroC


title: RNA-seq of Del(d1-d4) stembryos at 120h, rep1


title: RNA-seq of Del(d1-d4) stembryos at 96h, rep2


title: Injured Old C2

description: RNA was isolated from 3 mice


title: Hudep2_175_rep1_S3

description: MicroC


title: Injured Old C3

description: RNA was isolated from 3 mice


title: Injured Old C5

description: RNA was isolated from 3 mice


title: RNA-seq of Del(d1-d4) stembryos at 96h, rep1


title: RNA-seq of Del(CBS4) stembryos at 144h, rep1


title: Injured Old B10

description: RNA was isolated from 3 mice


title: Injured Old B12

description: RNA was isolated from 3 mice


title: Injured Old B7

description: RNA was isolated from 3 mice


title: RNA-seq of Del(CBS4) stembryos at 144h, rep2


title: Injured Old B9

description: RNA was isolated from 3 mice


title: Injured Old B6

description: RNA was isolated from 3 mice


title: Injured Old B8

description: RNA was isolated from 3 mice


title: Injured Old B5

description: RNA was isolated from 3 mice


title: Injured Old C8

description: RNA was isolated from 3 mice


title: Injured Old B3

description: RNA was isolated from 3 mice


title: Injured Old B4

description: RNA was isolated from 3 mice


title: RNA-seq of Del(CBS2) stembryos at 120h, rep2


title: Injured Old B2

description: RNA was isolated from 3 mice


title: RNA-seq of Del(CBS2) stembryos at 120h, rep1


title: Injured Old B1

description: RNA was isolated from 3 mice


title: Injured Old C1

description: RNA was isolated from 3 mice


title: RNA-seq of Del(CBS2) stembryos at 96h, rep1


title: Injured Old A11

description: RNA was isolated from 3 mice


title: Injured Old B11

description: RNA was isolated from 3 mice


title: Injured Old A8

description: RNA was isolated from 3 mice


title: RNA-seq of Del(CBS1) stembryos at 120h, rep2


title: RNA-seq of Del(CBS4) stembryos at 120h, rep2


title: Injured Old A9

description: RNA was isolated from 3 mice


title: RNA-seq of Del(CBS1) stembryos at 120h, rep1


title: Injured Old A6

description: RNA was isolated from 3 mice


title: Injured Old A7

description: RNA was isolated from 3 mice


title: Injured Old A5

description: RNA was isolated from 3 mice


title: RNA-seq of Del(CBS4) stembryos at 120h, rep1


title: RNA-seq of Del(CBS1) stembryos at 96h, rep2


title: Injured Old A3

description: RNA was isolated from 3 mice


title: Injured Old A4

description: RNA was isolated from 3 mice


title: Injured Old A2

description: RNA was isolated from 3 mice


title: RNA-seq of Del(CBS1) stembryos at 96h, rep1


title: Naïve Young H12

description: RNA was isolated from 5 mice

value: 3 months

value: Naïve


title: Naïve Young H10

description: RNA was isolated from 5 mice


title: Naïve Young H11

description: RNA was isolated from 5 mice


title: RNA-seq of Del(CBS1-5) stembryos at 144h, rep2


title: Injured Old A1

description: RNA was isolated from 3 mice


title: Injured Old A12

description: RNA was isolated from 3 mice


title: RNA-seq of Del(CBS1-5) stembryos at 144h, rep1


title: RNA-seq of Del(CBS2) stembryos at 96h, rep2


title: Naïve Young H9

description: RNA was isolated from 5 mice


title: Naïve Young H8

description: RNA was isolated from 5 mice


title: Injured Old A10

description: RNA was isolated from 3 mice


title: RNA-seq of Del(CBS1-5) stembryos at 120h, rep2


title: Naïve Young H7

description: RNA was isolated from 5 mice


title: Naïve Young H6

description: RNA was isolated from 5 mice


title: Naïve Young H5

description: RNA was isolated from 5 mice


title: Naïve Young H4

description: RNA was isolated from 5 mice


title: Naïve Young H3

description: RNA was isolated from 5 mice


title: RNA-seq of Del(CBS1-5) stembryos at 96h, rep2


title: RNA-seq of Del(CBS1-5) stembryos at 96h, rep1


title: Naïve Young H2

description: RNA was isolated from 5 mice


title: Naïve Young H1

description: RNA was isolated from 5 mice


title: Naïve Young G11

description: RNA was isolated from 5 mice


title: Naïve Young G9

description: RNA was isolated from 5 mice


title: Naïve Young G7

description: RNA was isolated from 5 mice


title: RNA-seq of Del(CBS1-2) stembryos at 120h, rep2


title: RNA-seq of Del(CBS1-2) stembryos at 120h, rep1


title: RNA-seq of Del(CBS1-2) stembryos at 96h, rep2


title: Naïve Young G6

description: RNA was isolated from 5 mice


title: RNA-seq of Del(CBS1-2) stembryos at 96h, rep1


title: Naïve Young G8

description: RNA was isolated from 5 mice


title: Naïve Young G5

description: RNA was isolated from 5 mice


title: Naïve Young G2

description: RNA was isolated from 5 mice


title: RNA-seq of wt stembryos at 120h, rep3


title: Naïve Young G3

description: RNA was isolated from 5 mice


title: RNA-seq of wt stembryos at 120h, rep4


title: RNA-seq of wt stembryos at 120h, rep2


title: Naïve Young F12

description: RNA was isolated from 5 mice


title: Naïve Young G1

description: RNA was isolated from 5 mice


title: Naïve Young F11

description: RNA was isolated from 5 mice


title: Naïve Young G12

description: RNA was isolated from 5 mice


title: RNA-seq of wt stembryos at 96h, rep4


title: RNA-seq of Del(CBS1-5) stembryos at 120h, rep1


title: 1,25OH2D3 DLAM rep2

city: Iwaki

first: Takahiro

last: Sawada

state: Fukushima

address: Jobankamiyunagayamachi Kaminodai57

country: Japan

institute: Research Institute of Innovative Medicine

data_processing:
Paired-end sequencing was performed on the DNBSEQ-G400RS High-throughput Sequencing Set
eads were mapped to the GRCh38.p13 (hg38) reference sequence using Bowtie2 (ver. 2.3.4.3)
Duplicate reads were removed using Picard (ver. 2.20.7) and samtools (ver. 1.9).
Peak calling was performed using MACS2 (ver. 2.2.4) with the default parameters.
The consistency of the peaks was evaluated by the irreproducible discovery rate using IDR (ver. 2.0.4.2).
Assembly: Peak annotation was conducted using HOMER (ver. 4.9.1) with the default settings.
Assembly: The differentially accessible peaks were obtained using DEseq2 (ver. 1.20.0).
Supplementary files format and content: tab-delimited text files include read counts values for each sample.

source_name: HaCaT

growth_protocol: HaCaT cells were seeded in 100 mm dishes in duplicate, and the culture medium was exchanged with FCS-free medium after 24 hours.

extract_protocol:
Prepare nuclei: To prepare nuclei, we spun 50,000 cells at 500 × g for 5 minutes, followed by a wash using 50 μL of cold 1x PBS and centrifugation at 500 × g for 5 minutes. Cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 × g for 10 minutes using a refrigerated centrifuge. To avoid losing cells during the nuclei prep, we used a fixed angle centrifuge and carefully pipetted away from the pellet after centrifugations.  Transpose and purify: Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase (Illumina) and 22.5 μL of nuclease free water). The transposition reaction was carried out for 30 minutes at 37 °C. Directly following transposition the sample was purified using a Qiagen Minelute kit.
Briefly, approximately 50,000 cells were lysed and the lysate subjected to a transposition reaction using Tn5 transposase (Illumina Catalog #FC121-1030) at 37°C for 30 minutes. The reaction liquid was purified using the Qiagen MinElute PCR Purification Kit. Then, five cycles of PCR were conducted using custom Nextera PCR primers and the NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolabs) [B]. The need for additional PCR cycles was determined by qPCR of the partially amplified products, following Wu and Buenrostro 2013. The PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter: A63881) by double size selection (left ratio: 1.4, right ratio: 0.5) according to the manufacturer’s protocol.

treatment_protocol: 1,25OH2D3 (final concentration: 100 nM) and/or DLAM-2b (final concentration: 1 μM) for 8 hours

value: HaCaT

value: Keratinocyte

value: add 100 nM 1,25OH2D3 and 1 uM DLAM-2b for 8h


title: Naïve Young G10

description: RNA was isolated from 5 mice


title: Naïve Young F10

description: RNA was isolated from 5 mice


title: RNA-seq of wt stembryos at 120h, rep1

value: stembryo

value: mES cells


title: RNA-seq of wt stembryos at 96h, rep3


title: 1,25OH2D3 DLAM rep1


title: Naïve Young F9

description: RNA was isolated from 5 mice


title: DLAM rep2

value: add 1 uM DLAM-2b for 8h


title: RNA-seq of wt stembryos at 96h, rep2


title: Naïve Young G4

description: RNA was isolated from 5 mice


title: DLAM rep1


title: Naïve Young F8

description: RNA was isolated from 5 mice


title: 1,25OH2D3 rep2

value: add 100 nM 1,25OH2D3 for 8h


title: RNA-seq of wt stembryos at 96h, rep1


title: Naïve Young F7

description: RNA was isolated from 5 mice


title: 1,25OH2D3 rep1


title: Naïve Young F6

description: RNA was isolated from 5 mice


title: RNA-seq of wt stembryos at 168h, Time-course_rep1


title: EtOH rep2

value: add EtOH for 8 h


title: Naïve Young F5

description: RNA was isolated from 5 mice

value: Spinal cord meninges


title: EtOH rep1


title: Naïve Young F4

description: RNA was isolated from 5 mice


title: Naïve Young F3

description: RNA was isolated from 5 mice


title: LETS1+Tb-rep2

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

institute: Leiden University Medical Center

data_processing:
RNA-Seq files were processed using the opensource BIOWDL RNAseq pipeline v4.0.0 (https://zenodo.org/record/3975552#.YiBgxIzMKV4) developed at the LUMC.
This pipeline performs FASTQ preprocessing (including quality control, quality trimming, and adapter clipping), RNA-Seq alignment, read quantification, and optionally transcript assembly.
FastQC was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.10) with default settings.
RNA-Seq reads’ alignment was performed using STAR (v2.7.5a) on GRCh38 human reference genome.
The gene read quantification was performed using HTSeq-count (v0.12.4) with setting “–stranded=no”. The gene annotation used for quantification was Ensembl version 99.
Assembly: GRCh38
Supplementary files format and content: raw read count in TSV format

growth_protocol: A549 cells were purchased from American Type Culture Collection (ATCC) and cultured in Dulbecco’s modified Eagle medium (DMEM; Thermo Fisher Scientific; 41965062) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific; 16000044) and 100 U/mL penicillin/streptomycin (Thermo Fisher Scientific; 15140163).

extract_protocol:
RNA was extracted by a NucleoSpin RNA kit (Macherey Nagel; Cat. Nr.: 740955) according to the manufacturer's instructions.
Library preparation and sequencing were performed by Beijing Genomics Institute (BGI) in China using the DNBSEQ platform.

treatment_protocol:
Transduced with expressing construct for LETS1 and treated with TGF-beta (5 ng/mL) for 4 h
Cells were transduced with lentiviral expressing constructs overnight. After two days culture, 1 ng/mL puromycin was added to the medium for selecting stable cells. After another 3 days culture, cells were treated with ligand buffer (-TGF-beta) or TGF-beta (5 ng/mL) for 4 h

value: human lung adenocarcinoma cells

value: LETS1 overexpression

value: TGF-beta


title: LETS1+Tb-rep3


title: LETS1+Tb-rep1


title: RNA-seq of wt stembryos at 144h, rep2


title: Naïve Young F2

description: RNA was isolated from 5 mice

value: Lymphatic endothelial cells

value: female


title: RNA-seq of wt stembryos at 132h, Time-course_rep2

value: wt


title: RNA-seq of wt stembryos at 144h, rep1


title: Naïve Young F1

description: RNA was isolated from 5 mice

value: 3 months


title: LETS1-Tb-rep3

treatment_protocol:
Transduced with expressing construct for LETS1 and treated with ligand buffer for 4 h
Cells were transduced with lentiviral expressing constructs overnight. After two days culture, 1 ng/mL puromycin was added to the medium for selecting stable cells. After another 3 days culture, cells were treated with ligand buffer (-TGF-beta) or TGF-beta (5 ng/mL) for 4 h

value: control


title: Naïve Young E12

description: RNA was isolated from 5 mice

value: Naïve


title: LETS1-Tb-rep2


title: RNA-seq of wt stembryos at 132h, Time-course_rep1


title: Naïve Young E10

description: RNA was isolated from 5 mice


title: RNA-seq of wt stembryos at 168h, Time-course_rep2


title: RNA-seq of wt stembryos at 108h, Time-course_rep2


title: LETS1-Tb-rep1


title: Naïve Young E11

description: RNA was isolated from 5 mice


title: Naïve Young E9

description: RNA was isolated from 5 mice


title: Co.vec+Tb-rep3

treatment_protocol:
Transduced with expressing construct for an empty vector of pCDH-EF1a-PURO and treated with TGF-beta (5 ng/mL) for 4 h
Cells were transduced with lentiviral expressing constructs overnight. After two days culture, 1 ng/mL puromycin was added to the medium for selecting stable cells. After another 3 days culture, cells were treated with ligand buffer (-TGF-beta) or TGF-beta (5 ng/mL) for 4 h


title: Co.vec+Tb-rep1


title: Co.vec+Tb-rep2


title: RNA-seq of wt stembryos at 108h, Time-course_rep1


title: Co.vec-Tb-rep3

treatment_protocol:
Transduced with expressing construct for an empty vector of pCDH-EF1a-PURO and treated with ligand buffer for 4 h
Cells were transduced with lentiviral expressing constructs overnight. After two days culture, 1 ng/mL puromycin was added to the medium for selecting stable cells. After another 3 days culture, cells were treated with ligand buffer (-TGF-beta) or TGF-beta (5 ng/mL) for 4 h


title: Naïve Young E8

description: RNA was isolated from 5 mice


title: RNA-seq of wt stembryos at 96h, Time-course_rep1


title: Co.vec-Tb-rep2


title: Naïve Young E5

description: RNA was isolated from 5 mice


title: RNA-seq of wt stembryos at 96h, Time-course_rep2


title: RNA-seq of wt stembryos at 84h, Time-course_rep2


title: Co.vec-Tb-rep1


title: RNA-seq of wt stembryos at 84h, Time-course_rep1


title: Naïve Young E4

description: RNA was isolated from 5 mice


title: Naive_S8

city: Tampere

first: Markus

middle: Juhani Tapani

last: Ojanen

address: Arvo Ylpön katu 34

country: Finland

institute: Tampere University

data_processing:
Quality control steps and alignment for sequenced reads was performed with  Snakemake 5.6.0 combining the relevant modules (FASTQC, TrimGalore!, STAR) from Snakemake-wrapper release 0.38.0 with in-house scripts.
Differential expression (DE) analysis in gene level was performed with DEseq2 1.24.0. Matrix was prefiltered by rowsum (threshold 10). Dataset was splitted by threatment and the cases analyzed separately because of variation.
Result tables were annotated with bioMart, ranked by p-value and merged with the DESeq2 abundance measures for samples.
Genome_build: GRCm38 (ENSEMBL release 97)
Supplementary_files_format_and_content: Matrix table with raw gene counts from STAR for every gene and every sample
Supplementary_files_format_and_content: Excel tables containing ranked DEGs and DEseq2 abundance measurements for each comparison

source_name: Naive CD8+ T cells

growth_protocol: Ex vivo cells were used in the experiment.

extract_protocol:
Naive CD8+ T cells from spleen and lymph nodes were sorted using fluorescence-activated cell sorting (FACS). Cells were washed with PBS, suspended in RLT lysis buffer (Qiagen) and the total RNA was exctracted using RNEasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Prior FACS the CD8+ T cells were enriched using CD8a  + T Cell Isolation Kit, mouse (Miltenyi)

tag: background strain

value: 8 weeks

value: Furin KO

tag: mouse sex

value: male


title: Naive_S7


title: RNA-seq of wt stembryos at 72h, Time-course_rep2

value: stembryo

value: mES cells


title: Naive_S6

value: WT


title: Naïve Young E3

description: RNA was isolated from 5 mice


title: H3K27ac HiChIP of wt stembryos at 120h

data_processing:
All scripts are available on https://github.com/lldelisle/scriptsForRekaikEtAl2022
TruSeq adapters were removed with cutadapt (Martin et al 2011) version 1.16 on each read independently (-a 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' for R1 and -a 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT' for R2).
Trimmed reads were processed with HiCUP version 0.6.1 (doi: 10.12688/f1000research.7334.1) with default paramters on mm10 or on the corresponding mutant genome.
The output BAM was converted to Juicebox format thanks to a custom python script available in  https://testtoolshed.g2.bx.psu.edu/repository/download?repository_id=be5040251cd4afb7&changeset_revision=44365a4feb3b&file_type=gz
Only pairs with both mates with quality above 30 were kept.
Filtered pairs were loaded into a 10kb matrix with cooler version 0.7.4 (Abdennur, N., and Mirny, L. (2019), https://doi.org/10.1093/bioinformatics/btz540).
Assembly: mm10
Supplementary files format and content: *.cool: raw matrix
Library strategy: HiChIP

extract_protocol:
Wild type stembryos were collected at 120h and fixed for 10 min in 1% formaldehyde at room temperature before proceeding with the library generation.
The protocol for H3K27ac HiChIP was adapted from (Mumback et al., 2016 doi: 10.1038/nmeth.3999). Briefly, after lysis, DpnII digestion, biotin fill-in and blunt-end ligation (see Capture Hi-C), samples were sonicated in a Covaris E220 instrument for 10 min (duty cycle 2%, peak incident power 105 W) and incubated overnight at 4° with magnetic beads conjugated to the H3K27ac antibody (Abcam, ab4729). The next day, beads were washed as described in ChIP protocol before elution of DNA fragments. A biotin pull-down was then performed (Dynabeads MyOne Streptavidin T1) followed by a TruSeq library preparation using fragments bound to the streptavidin beads. A qPCR was used to estimate library depth before final amplification with the Kapa HiFi library kit. Library was purified, size selected and quality assessed with fragment analyzer

value: H3K27ac (Abcam, #ab4729)


title: RNA-seq of wt stembryos at 72h, Time-course_rep1


title: Naïve Young E2

description: RNA was isolated from 5 mice

value: Spinal cord meninges


title: Naive_S5


title: Naïve Young E7

description: RNA was isolated from 5 mice


title: Naïve Young E1

description: RNA was isolated from 5 mice


title: Naïve Young D12

description: RNA was isolated from 5 mice


title: Naive_S4


title: Naïve Young D11

description: RNA was isolated from 5 mice


title: Naïve Young E6

description: RNA was isolated from 5 mice


title: RAD21 ChIP-M of wt stembryos at 144h, rep2

value: RAD21 (ab992, Abcam)


title: Naive_S2

value: 7 weeks


title: RAD21 ChIP-M of wt stembryos at 96h, rep2


title: Naïve Young D9

description: RNA was isolated from 5 mice


title: Naive_S3


title: Naive_S1


title: Naïve Young D8

description: RNA was isolated from 5 mice


title: RAD21 ChIP-M of wt stembryos at 168h, rep1


title: RAD21 ChIP-M of wt stembryos at 144h, rep1


title: RAD21 ChIP-M of wt stembryos at 132h, rep1


title: Acomys DMSO 24hpi, biological replicate 4

city: Utrecht

first: Antonio

last: Tomasso

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Data were processed according to the Lexogen Services pipeline for QuantSeq 3' mRNA Seq from Lexogen (https://www.lexogen.com/quantseq-3mrna-sequencing/), https://www.lexogen.com/wp-content/uploads/2018/09/015UG110V0111_QuantSeq-FWD-HT.pdf).
The alignment was performed with the Spliced Transcripts Alignment to a Reference (STAR) tool.
The RNA-Seq Quality Control package (RSeQC) was run to comprehensively evaluate the RNA-Seq data.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files contains gene counts

organism: Acomys cahirinus

source_name: punched ear pinna skin

extract_protocol:
The tissue was snap frozen, total RNA was extracted in Trizol (Life Technologies) according to manufacturer’s instructions
The extracted RNA samples were processed by Lexogen Services. The library was prepared through Lexogen QuantSeq FWD -SR75- kit, Product No. LS832303, according to manufacturer's instructions

treatment_protocol: The pERK inhibitor and relative DMSO control were injected from D12 to D15.

value: punched ear pinna skin

tag: strain

value: wild-type

tag: developmental stage

value: adult

tag: time point

value: DMSO control


title: Naïve Young D7

description: RNA was isolated from 5 mice

value: 3 months

value: Lymphatic endothelial cells

value: female


title: Acomys DMSO 24hpi, biological replicate 3


title: Naïve Young D6

description: RNA was isolated from 5 mice

value: Naïve


title: RAD21 ChIP-M of wt stembryos at 84h, rep1

value: wt

tag: stage (in_hours_after_aggregation)

tag: chip antibody


title: Acomys DMSO 24hpi, biological replicate 2

tag: tissue


title: Naïve Young D4

description: RNA was isolated from 5 mice

tag: age

tag: cell type


title: RAD21 ChIP-M of wt stembryos at 108h, rep1

tag: genotype


title: Naïve Young D2

description: RNA was isolated from 5 mice

tag: Sex

tag: sample group


title: Naïve Young D3

description: RNA was isolated from 5 mice


title: Acomys PD 24hpi, biological replicate 2

tag: treatment

value: pERK inhibitor


title: Acomys PD 24hpi, biological replicate 3


title: Acomys DMSO 24hpi, biological replicate 1


title: Naïve Young D10

description: RNA was isolated from 5 mice


title: RAD21 ChIP-M of wt stembryos at 72h, rep1

value: stembryo


title: Naïve Young D1

description: RNA was isolated from 5 mice


title: RAD21 ChIP-M of Del(CBS1-5) stembryos at 120h

value: mES cells


title: Acomys DMSO 15dpi, biological replicate 5


title: Naïve Young C12

description: RNA was isolated from 5 mice


title: PolII Ser2-p ChIP of wt stembryos at 144h, rep3

value: PolII Ser-2p (04-1571, Millipore)


title: PolII Ser2-p ChIP of wt stembryos at 144h, rep2


title: Naïve Young C11

description: RNA was isolated from 5 mice


title: Acomys DMSO 15dpi, biological replicate 3


title: Naïve Young C10

description: RNA was isolated from 5 mice


title: Acomys DMSO 15dpi, biological replicate 2


title: PolII Ser2-p ChIP of wt stembryos at 96h


title: Naïve Young D5

description: RNA was isolated from 5 mice


title: Naïve Young C9

description: RNA was isolated from 5 mice


title: Acomys DMSO 15dpi, biological replicate 1


title: PolII Ser2-p ChIP of wt stembryos at 84h


title: Naïve Young C8

description: RNA was isolated from 5 mice


title: Acomys PD 24hpi, biological replicate 1


title: Acomys PD 15dpi, biological replicate 5


title: Naïve Young C7

description: RNA was isolated from 5 mice


title: PolII Ser2-p ChIP of wt stembryos at 144h, rep1


title: Acomys PD 15dpi, biological replicate 4


title: Acomys DMSO 15dpi, biological replicate 4


title: Naïve Young C4

description: RNA was isolated from 5 mice


title: Naïve Young C5

description: RNA was isolated from 5 mice


title: Naïve Young C6

description: RNA was isolated from 5 mice


title: PolII ChIP-M of wt stembryos at 120h

value: PolII (ab817, Abcam)


title: 175_S1

description: CIRCLE-seq

data_processing:
Data were processed using https://github.com/tsailabSJ/changeseq
Assembly: hg38
Library strategy: CIRCLE-seq

extract_protocol:
Genomic DNA from HEK293T cells was isolated using a Gentra Puregene Kit (QIAGEN) according to the manufacturer’s instructions.
Purified genomic DNA was sheared with a Covaris S2 instrument to an average length of 300 bp. The fragmented DNA was end repaired, A-tailed and ligated to an uracil-containing stem-loop adaptor, using the KAPA HTP Library Preparation Kit, PCR Free (KAPA Biosystems). Adaptor-ligated DNA was treated with Lambda Exonuclease (NEB) and E. coli Exonuclease I (NEB) and then with USER enzyme (NEB) and T4 polynucleotide kinase (NEB). Intramolecular circularization of the DNA was performed with T4 DNA ligase (NEB) and residual linear DNA was degraded by Plasmid-Safe ATP-dependent DNase (Lucigen). In vitro cleavage reactions were performed with 125 ng Plasmid-Safe-treated circularized DNA, 90 nM Cas9-NG protein, Cas9 nuclease buffer (NEB) and 90 nM synthetic chemically modified sgRNA (-175), in a 50 μl volume. Cleaved products were A-tailed, ligated with a hairpin adaptor (NEB), treated with USER enzyme (NEB) and amplified by PCR with barcoded universal primers (NEBNext Multiplex Oligos for Illumina (NEB), using Kapa HiFi Polymerase (KAPA Biosystems).

tag: cell line


title: PolII ChIP-M of wt stembryos at 168h


title: Acomys PD 15dpi, biological replicate 2


title: PolII ChIP-M of wt stembryos at 132h


title: Acomys PD 15dpi, biological replicate 3


title: Acomys PD 15dpi, biological replicate 1


title: Naïve Young C1

description: RNA was isolated from 5 mice

value: Spinal cord meninges


title: PolII Ser2-p ChIP of wt stembryos at 72h


title: PolII ChIP-M of wt stembryos at 84h


title: PolII Ser2-p ChIP of wt stembryos at 120h


title: PolII ChIP-M of wt stembryos at 72h


title: Naïve Young B12

description: RNA was isolated from 5 mice


title: G3BP_KO_NTF2-rescue_NaAsO2_rep1

city: Princeton

first: Ralph

middle: E

last: Kleiner

state: NJ

address: Frick Laboratory on Washington Rd

department: Chemistry

institute: Princeton University

description: G3BP_KO_DESeq2_NTF2_rescue_stress_vs_NTF2_rescue.tabular

data_processing:
Alignment with STAR (v.1.5.3 and v2.7.0f)
Nucleotide frequency at each position in the transcriptome was uploaded to MySQL database.
A-to-I mutations were detected by comparing the nucleotide frequencies in each sample with the background control.
Differential expression with DESeq2 (v.2.11.40.6)
Assembly: CRCh38
Supplementary files format and content: For bedgraph files, first three columns denote genomic coordinates of edit sites. The fourth column represents the editing percentages of edit sites.
Supplementary files format and content: Tabular files are output of DESeq2.

molecule: polyA RNA

growth_protocol: All cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1x penicillin-streptomycin, and 2mM L-glutamine in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with TRIzol reagent (Thermo Fisher), and poly-A RNA was isolated using oligo-(dT) beads (NEB).
All libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

value: Bone osteosarcoma epithelial cells

value: G3BP1/2 knockout

value: Transient transfection, sodium arsenite treatment

tag: condition

value: Lipofectamine transfection of NTF2 deletion mutant G3BP1 transgene, 200 uM sodium arsenite

tag: time

value: 24 hour post-transfection, 2 hours for sodium arsenite


title: G3BP_KO_NTF2-rescue_NaAsO2_rep2


title: G3BP_KO_NTF2-rescue_rep2

description: G3BP_KO_DESeq2_NTF2_rescue_vs_KO.tabular

value: Transient transfection

value: Lipofectamine transfection of NTF2 deletion mutant G3BP1 transgene

value: 24 hour post-transfection


title: PolII ChIP-M of wt stembryos at 144h


title: NIPBL ChIP-M of wt stembryos at 168h

value: NIPBL (A301-779A, Bethyl Laboratories)


title: Naïve Young B11

description: RNA was isolated from 5 mice

value: 3 months

value: Lymphatic endothelial cells

value: female

value: Naïve


title: Naïve Young C3

description: RNA was isolated from 5 mice


title: G3BP_KO_NTF2-rescue_rep1


title: Naïve Young B10

description: RNA was isolated from 5 mice


title: NIPBL ChIP-M of wt stembryos at 144h

value: stembryo

value: mES cells

value: wt


title: NIPBL ChIP-M of wt stembryos at 132h


title: PolII ChIP-M of wt stembryos at 108h

value: PolII (ab817, Abcam)


title: G3BP_KO_WT-rescue_NaAsO2_rep1

description: G3BP_KO_DESeq2_WT_rescue_stress_vs_WT_rescue.tabular

value: Bone osteosarcoma epithelial cells

value: Lipofectamine transfection of WT G3BP1 transgene, 200 uM sodium arsenite


title: Naïve Young C2

description: RNA was isolated from 5 mice

value: Spinal cord meninges


title: PolII ChIP-M of wt stembryos at 96h


title: Naïve Young B9

description: RNA was isolated from 5 mice


title: G3BP_KO_WT-rescue_NaAsO2_rep2

value: G3BP1/2 knockout

value: Transient transfection, sodium arsenite treatment


title: G3BP_KO_WT-rescue_rep2

value: Transient transfection

value: Lipofectamine transfection of WT G3BP1 transgene


title: NIPBL ChIP-M of wt stembryos at 120h


title: Naïve Young B7

description: RNA was isolated from 5 mice


title: Naïve Young B8

description: RNA was isolated from 5 mice


title: G3BP_KO_WT-rescue_rep1

value: 24 hour post-transfection


title: NIPBL ChIP-M of wt stembryos at 108h

value: NIPBL (A301-779A, Bethyl Laboratories)


title: NIPBL ChIP-M of wt stembryos at 96h


title: G3BP_KO_NaAsO2_rep2

value: Sodium arsenite treatment

value: 200 uM sodium arsenite

value: 2 hours for sodium arsenite


title: Naïve Young B6

description: RNA was isolated from 5 mice

value: 3 months

value: Lymphatic endothelial cells

value: female

value: Naïve


title: NIPBL ChIP-M of wt stembryos at 84h

value: stembryo

value: mES cells

value: wt


title: Naïve Young B5

description: RNA was isolated from 5 mice

value: Spinal cord meninges


title: G3BP_KO_NaAsO2_rep1

value: Bone osteosarcoma epithelial cells

value: G3BP1/2 knockout


title: Naïve Young B4

description: RNA was isolated from 5 mice


title: Naïve Young B3

description: RNA was isolated from 5 mice


title: Naïve Young B2

description: RNA was isolated from 5 mice


title: G3BP_KO_rep2


title: H3K27me3 ChIP of wt stembryos at 96h, rep2

value: H3K27me3 (39155, Active Motif)


title: G3BP_KO_rep1


title: NIPBL ChIP-M of wt stembryos at 72h


title: Naïve Young B1

description: RNA was isolated from 5 mice


title: TRIBE-ID_YBX1_no_treament_rep2

source_name: FlpIn 293 Trex

value: FlpIn 293 Trex

value: Embryonic kidney cells

value: Stable expression of YBX1-FRB and FKBP-ADAR

value: Tetracycline induction

value: 1ug/mL tetracycline

value: 24 hour for tetracycline


title: H3K27me3 ChIP of wt stembryos at 96h, rep1


title: H3K27me3 ChIP of Del(CBS1-5) stembryos at 96h, rep2


title: H3K27me3 ChIP of Del(CBS1-5) stembryos at 96h, rep1


title: TRIBE-ID_YBX1_no_treament_rep1


title: TRIBE-ID_YBX1_2hr_rapamycin_NaAsO2_rep2

value: Tetracycline induction, rapamycin and sodium arsenite treatment

value: 1ug/mL tetracycline, 100 nM rapamycin, 200 uM sodium arsenite

value: 24 hour for tetracycline, 2 hour for rapamycin and sodium arsenite


title: Naïve Young A10

description: RNA was isolated from 5 mice

value: 3 months

value: Lymphatic endothelial cells

value: female

value: Naïve


title: Naïve Young A11

description: RNA was isolated from 5 mice

value: Spinal cord meninges


title: Naïve Young A12

description: RNA was isolated from 5 mice


title: TRIBE-ID_YBX1_2hr_rapamycin_NaAsO2_rep1


title: Naïve Young A9

description: RNA was isolated from 5 mice


title: H3K27me3 ChIP of wt stembryos at 144h

value: stembryo

value: mES cells

value: wt


title: TRIBE-ID_YBX1_2hr_rapamycin_rep1

value: FlpIn 293 Trex

value: Tetracycline induction, rapamycin treatment

value: 1ug/mL tetracycline, 100 nM rapamycin

value: 24 hour for tetracycline, 2 hour for rapamycin


title: TRIBE-ID_YBX1_2hr_rapamycin_rep2

value: Embryonic kidney cells

value: Stable expression of YBX1-FRB and FKBP-ADAR


title: H3K27me3 ChIP of wt stembryos at 120h

value: H3K27me3 (39155, Active Motif)


title: H3K27me3 ChIP of wt stembryos at 96h


title: H3K27me3 ChIP of wt stembryos at 72h


title: Naïve Young A7

description: RNA was isolated from 5 mice


title: TRIBE-ID_1hr_rapamycin_NaAsO2_rep1

value: Stable expression of G3BP1-FRB and FKBP-ADAR

value: Tetracycline induction, rapamycin and sodium arsenite treatment

value: 1ug/mL tetracycline, 100 nM rapamycin, 200 uM sodium arsenite

value: 24 hour for tetracycline, 1 hour for rapamycin and sodium arsenite


title: Naïve Young A8

description: RNA was isolated from 5 mice

value: 3 months

value: Lymphatic endothelial cells

value: female


title: TRIBE-ID_1hr_rapamycin_NaAsO2_rep2


title: Naïve Young A6

description: RNA was isolated from 5 mice

value: Spinal cord meninges

value: Naïve


title: H3K27ac ChIP of wt stembryos at 120h, rep2

value: stembryo

value: mES cells

value: wt

value: H3K27ac (ab4729, Abcam)


title: H3K27ac ChIP of wt stembryos at 120h, rep1


title: H3K27ac ChIP of Del(CBS1) stembryos at 120h, rep2


title: Naïve Young A5

description: RNA was isolated from 5 mice


title: Naïve Young A4

description: RNA was isolated from 5 mice


title: H3K27ac ChIP of Del(CBS1) stembryos at 120h, rep1


title: TRIBE-ID_30min_rapamycin_NaAsO2_rep2

value: FlpIn 293 Trex

value: 24 hour for tetracycline, 30 minutes for rapamycin and sodium arsenite


title: Naïve Young A3

description: RNA was isolated from 5 mice


title: Naïve Young A2

description: RNA was isolated from 5 mice


title: H3K27ac ChIP of wt stembryos at 96h, rep2


title: H3K27ac ChIP of wt stembryos at 96h, rep1


title: d15_4028_RNA_S10

city: Pittsburgh

first: Daniella

last: Schwartz

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422
Reads of 50 bases were processed using the rna-seek pipeline (https://ccbr.github.io/RNA-seek/): adapter sequences were trimmed with cutadapt 1.18
Reads were mapped to the mouse transcriptome and genome mm10 or human transcriptome and genome GRCh38 (hg38) using STAR.
Gene expression values (FPKM: Fragments Per Kilobase exon Per Million mapped reads; TPM, Tags Per Million mapped reads; counts) were generated using RSEM.
Differential gene expression was calculated using DESeq2.
Assembly: mm10 (mouse), hg38 (human)
Supplementary files format and content: FPKM_all_samples_RSEM

source_name: In vitro differentiated Th9 (d15)

growth_protocol: Complete RPMI-1640 with glutamine (10% FBS, 100 IU/mL penicillin, 0.1 mg/mL streptomycin)

extract_protocol:
Cells were suspended in Trizol LS (Invitrogen), and total RNA extracted according to the manufacturer instruction.
Libraries for mRNA-sequencing were prepared using the NEBNext Ultra II Directional RNAseq Library preparation kit, per the manufacturer’s instructions.

treatment_protocol: Human peripheral blood mononuclear cells (PBMC) were isolated by density centrifugation (Ficoll-Paque). Naïve human CD4+ T cells were magnetically enriched to >95% purity (StemCell) and plated at a density of 1 x10^6 in the presence of cytokines and antibodies to promote the differentiation of Th9 (1 μg/mLCD28, 2.5 μg/mL IFN-γ, 5 ng/mL hTGFβ, 10 ng/mL hIL-2, 30 ng/mL hIL-4, 10 ng/mL hIL-1β)After 5 days, cells were washed and cultured without aCD3 or aCD28 but with all polarizing cytokines and antibodies for an additional 10 days (media, cytokines, and antibodies changed every 2 days, total 15 days of culture)

value: In vitro differentiated Th9 (d15)


title: TRIBE-ID_30min_rapamycin_NaAsO2_rep1

value: Embryonic kidney cells


title: H3K27ac ChIP of Del(CBS1) stembryos at 96h, rep2


title: H3K27ac ChIP of Del(CBS1) stembryos at 96h, rep1


title: d15_3822_RNA_S22


title: Naïve Young A1

description: RNA was isolated from 5 mice


title: Naïve Old H12

description: RNA was isolated from 5 mice

value: 24 months


title: Naïve Old H11

description: RNA was isolated from 5 mice


title: H3K27ac ChIP of wt stembryos at 168h


title: d15_3692_RNA_S16


title: Naïve Old H10

description: RNA was isolated from 5 mice


title: H3K27ac ChIP of wt stembryos at 144h


title: d8_4031_RNA_S3

source_name: In vitro differentiated Th9 (d8)

treatment_protocol: Human peripheral blood mononuclear cells (PBMC) were isolated by density centrifugation (Ficoll-Paque). Naïve human CD4+ T cells were magnetically enriched to >95% purity (StemCell) and plated at a density of 1 x10^6 on plate-bound aCD3 (1 μg/mL, OKT3), in the presence of cytokines and antibodies to promote the differentiation of Th9 (1 μg/mL aCD28, 2.5 μg/mL aIFN-γ, 5 ng/mL hTGFβ, 10 ng/mL hIL-2, 30 ng/mL hIL-4, 10 ng/mL hIL-1β) for 5 days. After 5 days, cells were washed and cultured without aCD3 or aCD28 but with all polarizing cytokines and antibodies for an additional 3 days (media, cytokines, and antibodies changed every 2 days, total 8 days of culture)

value: In vitro differentiated Th9 (d8)


title: H3K27ac ChIP of wt stembryos at 132h


title: d8_4028_RNA_S9


title: Naïve Old H9

description: RNA was isolated from 5 mice


title: Naïve Old H8

description: RNA was isolated from 5 mice


title: TRIBE-ID_15min_rapamycin_NaAsO2_rep2

value: Stable expression of G3BP1-FRB and FKBP-ADAR

value: Tetracycline induction, rapamycin and sodium arsenite treatment

value: 1ug/mL tetracycline, 100 nM rapamycin, 200 uM sodium arsenite

value: 24 hour for tetracycline, 15 minutes for rapamycin and sodium arsenite


title: H3K27ac ChIP of wt stembryos at 120h


title: d8_3822_RNA_S21


title: TRIBE-ID_15min_rapamycin_NaAsO2_rep1


title: Naïve Old H7

description: RNA was isolated from 5 mice

value: Lymphatic endothelial cells

value: female


title: d15_4031_RNA_S4


title: H3K27ac ChIP of wt stembryos at 108h


title: Naïve Old H6

description: RNA was isolated from 5 mice

value: Spinal cord meninges

value: Naïve


title: d8_3692_RNA_S15


title: Naïve Old H5

description: RNA was isolated from 5 mice


title: H3K27ac ChIP of wt stembryos at 84h

value: stembryo

value: mES cells


title: d5_4031_RNA_S2

source_name: In vitro differentiated Th9 (d5)

treatment_protocol: Human peripheral blood mononuclear cells (PBMC) were isolated by density centrifugation (Ficoll-Paque). Naïve human CD4+ T cells were magnetically enriched to >95% purity (StemCell) and plated at a density of 1 x10^6 on plate-bound aCD3 (1 μg/mL, OKT3), in the presence of cytokines and antibodies to promote the differentiation of Th9 (1 μg/mL aCD28, 2.5 μg/mL aIFN-γ, 5 ng/mL hTGFβ, 10 ng/mL hIL-2, 30 ng/mL hIL-4, 10 ng/mL hIL-1β) for 5 days

value: In vitro differentiated Th9 (d5)


title: d5_3822_RNA_RNA_S20


title: d5_3692_RNA_S14


title: H3K27ac ChIP of wt stembryos at 96h

value: wt

value: H3K27ac (ab4729, Abcam)


title: H3K27ac ChIP of wt stembryos at 72h


title: Naïve Old H4

description: RNA was isolated from 5 mice


title: d5_4028_RNA_S8


title: H3K27ac ChIP of wt stembryos at 48h


title: CTCF ChIP-M of wt stembryos at 168h

value: CTCF (61311, Active Motif)


title: Naïve Old H2

description: RNA was isolated from 5 mice


title: Naïve Old H1

description: RNA was isolated from 5 mice


title: Naïve Old H3

description: RNA was isolated from 5 mice


title: naive_4028_RNA_S7

source_name: naive T cells

treatment_protocol: Human peripheral blood mononuclear cells (PBMC) were isolated by density centrifugation (Ficoll-Paque). Naïve human CD4+ T cells were magnetically enriched to >95% purity (StemCell)

value: naive T cells


title: Naïve Old G12

description: RNA was isolated from 5 mice

value: 24 months


title: Naïve Old G11

description: RNA was isolated from 5 mice


title: naive_4031_RNA_S1


title: CTCF ChIP-M of wt stembryos at 72h


title: CTCF ChIP-M of Ins(2xCBS-d4d8) stembryos at 144h


title: CTCF ChIP-M of Del(CBS4) stembryos at 120h


title: Naïve Old G10

description: RNA was isolated from 5 mice


title: CTCF ChIP-M of Del(CBS2) stembryos at 96h


title: Naïve Old G9

description: RNA was isolated from 5 mice


title: CTCF ChIP-M of Del(CBS1) stembryos at 96h


title: 4213_d8_K4me3_S23

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422
Reads of 50 bases were processed using the ccbr pipeliner tool (https://ccbr.github.io/pipeliner-docs/): adapter sequences were trimmed with cutadapt 1.18
Data were mapped to the mouse genome mm10 or human genome GRCh38 (hg38)  using BWAmem 0.7.17. Uniquely mapped and nonredundant reads were generated using Picard 2.17.11 and used for downstream analysis.
The aligned files were converted to bam format using SAMtools 1.6, and bigwig files were created using deepTools 3.0.1.
For downstream analysis, peaks were called using MACS v2.1.1 using a FDR 0.01 and with the input sample for background correction and using the --broad setting
Assembly: mm10 (mouse), hg38 (human)
Supplementary files format and content: bedfile, broadPeak

extract_protocol:
ChIP-seq sample preparation was performed with Covaris kit (PN 520154). Naïve T cells were cultured in vitro under Th9 promoting conditions and treated with chemical cross-linking (1% formaldehyde) on days 0, 3, 4, and 8 (murine) or days 0, 5, 8, and 15 (human). At least 0.5 million cells were used for each immunoprecipitation. After chemical chromatin cross-linking (1% formaldehyde), cells were washed and frozen at -80C. Cells were resuspended in Lysis Buffer B (Covaris) with protease inhibitors, and DNA fragmentation was performed on a Covaris Sonicator (ME220) for 8 min to an average length of 200-700 bp.  After sonication, cells were immunoprecipitated with anti-H3K27Ac (ab4729; Abcam), anti-H3K4Me1 (ab8895; Abcam), and anti-H3K4Me3 (ab8580; Abcam). Genomic DNA (input) was prepared by treating aliquots of chromatin with proteinase K, and heated for de-cross linking, followed by column-based DNA purification (28106, Qiagen).  An aliquot of chromatin underwent immunoprecipitation, after which decrosslinking was performed as above.
After recovering purified DNA, 5ng or more of DNA was used to generate libraries using the NEBNext Ultra Directional II DNA sequencing kit per the manufacturer’s instructions.

value: In vitro differentiated Th9 (d8)


title: Naïve Old G8

description: RNA was isolated from 5 mice


title: CTCF ChIP-M of Del(CBS1-5) stembryos at 96h

data_processing:
All scripts are available on https://github.com/lldelisle/scriptsForRekaikEtAl2022
Fastqs of the 3 replicates of wt_144h_pSer2PolII were concatenated before any processing.
Adapter sequences were trimmed from reads using cutadapt (Martin et al 2011) version 1.16 (-a 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC' -A 'GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT' for ChIP and -a 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC' -A 'CTGTCTCTTATACACATCTGACGCTGCCGACGA' for ChIPmentation).
Trimmed reads were mapped on mm10 genome or the mutant genome Ins(2xCBS-d4d8) for the corresponding  mutant CTCF ChIPmentation) using bowtie2 version 2.3.4.1 (Langmead et al. 2012).
Only aligments with proper pairs and mapping quality above 30 were kept using samtools 1.8.
Peaks and coverage were obtained with macs2 version 2.1.1.20160309 (--format BAMPE --gsize 1870000000 --call-summits --bdg).
In order to better compare ChIP, ChIP for the same protein with a time-course were normalized together using a custom python script (available in the github repository). Similarly, this normalization was used when mutant and control were performed in parallel (see supplementary table).
For H3K27ac and H3K27me3, in figure 7B and S10A, in order to reduce the impact of variations in gastruloid growth speed, the profile of mutant and corresponding wild-type were corrected using the time-course experiment and the profile around the HoxA cluster as a guide (see github repository for more details).
Assembly: mm10 or Ins(2xCBS-d4d8) for the sample Ins(2xCBS-d4d8)_144h_CTCF
Supplementary files format and content: *.narrowPeak.gz: narrowPeak from macs2
Supplementary files format and content: *.bigwig: macs2 coverage
Supplementary files format and content: *_Normalized.bigwig: macs2 coverage normalized between experiments for time-course or mutant and corresponding controls (see supplementary table)
Supplementary files format and content: *_Normalized_HCN_*h.bedgraph.gz: macs2 normalized coverage on the Hox clusters corrected for variation in gastroloid growth speeds using the profile around HoxA cluster and time-course as a guide

extract_protocol:
Collected stembryos were pooled in a 15 ml falcon tube, washed with PBS and resuspended in 1 ml PBS containing 1% formaldehyde for fixation during 10 min at room temperature. The crosslink reaction was stopped by adding a glycine solution to a final concentration of 0.125 M. Fixed stembryos were pelleted and stored at -80°C until further use.
ChIP and ChIP-M experiments were performed according to the protocol described in (Rodriguez-Carballo et al., 2017) and (Darbellay et al., 2019), and adapted for stembryos samples. Samples were resuspended in a sonication buffer (Tris HCl pH=8.0 50 mM; EDTA 10 mM; SDS 0.25% and protease inhibitors) and sonicated in a Covaris E220 device for 14 min (duty cycle 2%, peak incident power 105 W) to obtain an average chromatin fragment size of 300-500 bp. A dilution buffer (HEPES pH=7.3 20 mM; EDTA 1 mM; NP40 0.1%; NaCl 150 mM and protease inhibitors) was added to the sonicated chromatin and incubated with the antibody-bead complex (Pierce Protein A/G Magnetic Beads, Thermo Scientific) overnight at 4°C. Sequential washes were then performed twice with RIPA buffer (Tris HCl pH=8.0 10 mM; EDTA 1 mM; Sodium Deoxycholate 0.1% TritonX-100 1%; NaCl 140 mM and protease inhibitors), RIPA High salt buffer (Tris HCl pH=8.0 10 mM; EDTA 1 mM; Sodium Deoxycholate 0.1% TritonX-100 1%; NaCl 500 mM and protease inhibitors), LiCl buffer (Tris HCl pH=8.0 10 mM; EDTA 1 mM; LiCl 250 mM; Sodium Deoxycholate 0.5%; NP40 0.5% and protease inhibitors) and Tris HCl buffer (pH=8.0 10mM and protease inhibitors). For ChIP experiments (H3K27ac (ab4729, Abcam), H3K27me3 (39155, Active Motif), CDX2 (sc-393572, Santa Cruz) and PolII-Ser2p (04-1571, Millipore)), DNA fragments were incubated in the elution buffer (Tris HCl pH=8.0 10 mM; EDTA 5 mM; NaCl 300 mM and SDS 0.1%) containing proteinase K and purified using the Qiagen MiniElute kit. A phosphatase inhibitor (PhosStop, Roche) was used during PolII-Ser2p ChIP incubation and beads wash. The DNA library was produced using TruSeq adapters and amplified with the Kapa HiFi library kit (Roche) using a number of cycles determined by qPCR. For ChIP-M samples (CTCF (61311, Active Motif), PolII (ab817, Abcam), RAD21 (ab992, Abcam) and NIPBL (A301-779A, Bethyl Laboratories)), DNA fragments bound to the antibody-bead complex were tegmented using the Nextera Tegmentation kit. Beads were resuspended in the tegmentation buffer and incubated at 37° for 2 min with 1 µl of the Tn5 transposase. Fragment were then eluted and purified as described previously, and amplified using Nextera primers. Final DNA libraries were purified and size selected using AMPure XP magnetic beads (Beckman Coulter), and a fragment analysis was performed before sequencing


title: Naïve Old G7

description: RNA was isolated from 5 mice

data_processing:
Demultiplexing with custom Python and perl script
Aligned to the Ensembl release 76 top-level assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Assembly: mm10
Supplementary files format and content: raw gene counts for all cells

extract_protocol:
For the contusion injury, mice were anesthetized with ketamine (100 mg/kg)-xylazine (10 mg/kg) mixture. A 15-mm midline skin incision was made, and the connective tissue and muscles were bluntly dissected to expose T6-T13. Laminectomy was performed at T9 to expose the dorsal spinal cord, and the vertebral column was stabilized with angled clamps attached to the T7 and T12 transverse processes. The contusion injury was delivered using an Infinite Horizon Impactor (IH-0400 Impactor) with a force of 90 dynes. After injury, the muscles and skin were sutured separately. Mice were humanely euthanized with an intraperitoneal injection of a lethal dose of Euthasol® (10% v/v), followed by transcardiac perfusion of PBS with 5 U/mL of Heparin. Vertebral columns were obtained. The ventral bone of the vertebrae was cut laterally and was removed to expose the spinal cord. Nervous tissue was carefully dissected from the bone using fine forceps to release the dorsal root ganglia surrounded by the meninges. The meninges was cut along the ventral side and peeled from the spinal cord. Spinal cord meninges was enzymatically digested in RPMI containing 1 mg/mL collagenase VIII, 0.5 mg/mL DNase I, and 2% FBS for 30 minutes at 37°C with shaking. Samples were passed through a 70 µm filter to obtain single-cell suspensions, washed with FACS buffer, and pelleted at 380 xg for 5 minutes. Cells were resuspended in FACS buffer with 1:100 CD16/32 Fc block. They were stained with CD31, CD45, Podoplanin and Lyve1, washed, and resuspended in DAPI-containing FACS buffer. Single meningeal lymphatic endothelial cells were sorted as Live (DAPI-) CD45- CD31+ PDPN+ Lyve1+ cells using a FACS Aria II. Individual cells were sorted into 96-well plates containing 2 µL of 10X RNA lysis buffer (Takara) and 5% RNAse out (Takara) and rapidly frozen over dry ice.
Library preparation was performed with 2 µL of single cell lysates arrayed in 96-well PCR plates. ds-cDNA was prepared using a protocol adapted from the Takara-Clontech SMARTer methods. cDNA was blunt ended, had an A base added to the 3’ ends, and had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified using a standard Illumina i7 primer to introduce an index sequence and FACSseq Lib PCR 1.0 specific to fragments containing the cell barcode added during cDNA synthesis. Fragments were sequenced on an Illumina NovaSeq.


title: 4213_d8_K4me1_S22


title: CTCF ChIP-M of Del(CBS1-2) stembryos at 96h


title: Naïve Old G6

description: RNA was isolated from 5 mice


title: Naïve Old G5

description: RNA was isolated from 5 mice


title: naive_3822_RNA_S19


title: Naïve Old G4

description: RNA was isolated from 5 mice


title: CHi-C of wt stembryos at 120h

data_processing:
All scripts are available on https://github.com/lldelisle/scriptsForRekaikEtAl2022
TruSeq adapters were removed with cutadapt (Martin et al 2011) version 1.16 (-a 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' -A 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT').
Trimmed reads were processed with HiCUP version 0.6.1 (doi: 10.12688/f1000research.7334.1) with default paramters on mm10 or on the corresponding mutant genome.
The output BAM was converted to Juicebox format thanks to a custom python script available in  https://testtoolshed.g2.bx.psu.edu/repository/download?repository_id=be5040251cd4afb7&changeset_revision=44365a4feb3b&file_type=gz
Only pairs with both mates falling into the capture region (mm10:chr2:72402000-77000000) and with both mates with quality above 30 were kept.
Filtered pairs were loaded into 2kb and 5kb matrices with cooler version 0.7.4 (Abdennur, N., and Mirny, L. (2019), https://doi.org/10.1093/bioinformatics/btz540).
The matrices were balanced with cooler balance (--cis-only).
For the mutant Del(subTAD1), the balancing was done with the option --ignore-diags 5 instead of --ignore-diags 2 to discard the bias due to the presence of a BAC containing the region (mm10:chr2:74747769-74913171).
Assembly: mm10 for wt samples and Del(CBS*) samples and mutant genomes for Del(d1-d4) and Del(sub-TAD1)
Supplementary files format and content: *_validPairs_*.txt.gz: all valid pairs from HiCUP in juicebox format (<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse)   pos = middle of the fragment)
Supplementary files format and content: *_*kb_Balanced_*.cool: balanced matrix at 2 or 5kb-bins only in the captured region
Library strategy: Capture Hi-C


title: CHi-C of wt stembryos at 144h


title: CHi-C of wt stembryos at 168h


title: 4213_d5_K27Ac_S17


title: Naïve Old G3

description: RNA was isolated from 5 mice


title: naive_3692_RNA_S13


title: CHi-C of wt stembryos at 96h


title: Naïve Old G1

description: RNA was isolated from 5 mice


title: Naïve Old G2

description: RNA was isolated from 5 mice


title: 4213_d8_input_S7


title: 4213_d15_input_S10

value: In vitro differentiated Th9 (d15)


title: CHi-C of wt stembryos at 72h


title: 4213_d15_K4me3_S9


title: Naïve Old F12

description: RNA was isolated from 5 mice


title: CHi-C of wt stembryos at 48h


title: 4213_d8_K27Ac_S8


title: 4213_d15_K4me1_S2


title: 4213_d5_input_S20


title: Naïve Old F11

description: RNA was isolated from 5 mice


title: 4213_d15_K27Ac_S14


title: Naïve Old F10

description: RNA was isolated from 5 mice


title: CHi-C of Del(d1-d4) stembryos at 96h


title: CHi-C of Del(CBS1-5) stembryos at 168h


title: 4213_d5_K4me3_S15


title: 4213_Naive_input_S21


title: Naïve Old F9

description: RNA was isolated from 5 mice


title: 4213_d5_K4me1_S19


title: CHi-C of Del(CBS1-5) stembryos at 144h


title: Naïve Old F8

description: RNA was isolated from 5 mice


title: 4213_Naive_K4me3_S18


title: CHi-C of Del(CBS1-5) stembryos at 120h


title: Naïve Old F7

description: RNA was isolated from 5 mice


title: 4213_Naive_K4me1_S1


title: 4167_d8_input_S7


title: 4213_Naive_K27Ac_S28


title: Naïve Old F6

description: RNA was isolated from 5 mice


title: CHi-C of Del(sub-TAD1) stembryos at 96h


title: Naïve Old F5

description: RNA was isolated from 5 mice


title: 4167_d8_K4me3_S23


title: CHi-C of Del(CBS1-5) stembryos at 72h


title: WT mouse 5

city: Vancouver

first: Ben

last: Life

state: BC

address: 950 W 28th Ave

country: Canada

institute: University of British Columbia

description:
ghko_vs_wt_all_genes.txt
ghko_vs_wt_significant_genes.txt
het_vs_wt_all_genes.txt
het_vs_wt_significant_genes.txt

data_processing:
All RNA-seq data processing and statistical analyses were carried out using R (v. 4.1.2)
Expression counts were retrieved directly from the BaseSpace application (Illumina) and were visually inspected before and after normalization to detect any sample with uncommon overall expression profile
Differential expression (DE) analyses were performed using the DESeq2 R package (v.1.34.0)
P-values were adjusted using the Benjamini-Hochberg procedure to control False-discovery Rates at 5%.
No fold change cut-off was applied to the differentially expressed genes
Assembly: mm10
Supplementary files format and content: Processed data files contain pairwise comparisons of gene expression between genotypes
Supplementary files format and content: Tab delimited text files containing within genotype mean read counts and log fold change of mean read counts between the specified genotypes
Supplementary files format and content: Processed data files annotated as "significant_genes" contain only those genes identified as significantly differentially expressed at the adjusted p value threshold
Supplementary files format and content: Processed data files annotated "all_genes" contain expression information for all genes regardless of whether or not they meet the adjusted p value threshold

source_name: Cortex

extract_protocol:
RNA was extracted using PureLink RNA mini kit (Invitrogen). 200 ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer's protocols.

value: Cortex

value: male

value: Grn+/+

value: 18 months


title: 4167_d8_K4me1_S22


title: Naïve Old F4

description: RNA was isolated from 5 mice

value: Lymphatic endothelial cells

value: female


title: 4167_d8_K27Ac_S8


title: Naïve Old F2

description: RNA was isolated from 5 mice

value: Spinal cord meninges

value: Naïve


title: WT mouse 3


title: 4167_d5_input_S20


title: WT mouse 4


title: Naïve Old F3

description: RNA was isolated from 5 mice


title: Naïve Old F1

description: RNA was isolated from 5 mice


title: 4167_d5_K4me3_S15


title: Naïve Old E12

description: RNA was isolated from 5 mice


title: WT mouse 1


title: WT mouse 2


title: CHi-C of Del(CBS1-5) stembryos at 96h

value: stembryo

value: mES cells


title: 4167_d5_K4me1_S19

value: In vitro differentiated Th9 (d5)


title: Grn+/- mouse 4

description:
ghko_vs_het_all_genes.txt
ghko_vs_het_significant_genes.txt
het_vs_wt_all_genes.txt
het_vs_wt_significant_genes.txt

value: Grn+/-


title: Naïve Old E11

description: RNA was isolated from 5 mice


title: 4167_d5_K27Ac_S17


title: 4167_d15_input_S10


title: CHi-C of Del(CBS1-5) stembryos at 48h


title: Grn+/- mouse 3


title: Naïve Old E10

description: RNA was isolated from 5 mice


title: Grn+/- mouse 1


title: Grn+/- mouse 2


title: Naïve Old E8

description: RNA was isolated from 5 mice


title: 4167_d15_K4me1_S2


title: Grn-/-; GRNtg mouse 4

description:
ghko_vs_het_all_genes.txt
ghko_vs_het_significant_genes.txt
ghko_vs_wt_all_genes.txt
ghko_vs_wt_significant_genes.txt

value: Grn-/-; GRNtg


title: Naïve Old E7

description: RNA was isolated from 5 mice


title: 4167_d15_K27Ac_S14


title: Naïve Old E6

description: RNA was isolated from 5 mice


title: 4167_Naive_input_S21

value: naive T cells


title: Grn-/-; GRNtg mouse 3


title: Naïve Old E4

description: RNA was isolated from 5 mice

value: 24 months


title: Grn-/-; GRNtg mouse 2


title: 4167_Naive_K4me3_S18


title: Naïve Old E5

description: RNA was isolated from 5 mice


title: Naïve Old E3

description: RNA was isolated from 5 mice


title: 4167_Naive_K4me1_S1


title: 3500_Th1

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422
Redundant paired end (PE) reads were removed using fastquniq
PE reads of 50 bases were aligned to the mouse genome build mm10 or human build hg19 with Bowtie 0.12.8, following the guidelines presented by Buenrostro et al.
Customized python scripts were used to calculate fragment length of each pair of uniquely mapped PE reads for size distribution analysis, and to group uniquely mapped reads into bins of 0 to 175 bases and 180 to 250 bases, respectively.
UCSC Genome Browser viewable and normalized BigWig files were generated with the Hypergeometric Optimization of Motif EnRichment program (HOMER) version 4.8. Only one mapped read to each unique region of the genome that was less than 175 bp was kept and used in peak calling.
Regions of open chromatin were identified by MACS (version 1.4.2) using a p-value threshold of 1 × 10−5. Only regions called in both replicates were used in downstream analysis. Peak intensities (“tags” column) were normalized as tags per 10 million reads (RP10M) in the original library. Signal across all sites (i.e., all annotated genes and all accessible chromatin regions) was analyzed to eliminate potential bias by pre-selection.
Assembly: mm10 (mouse), hg19 (human)
Supplementary files format and content: bigWig, narrowPeak

source_name: In vitro differentiated Th1 (d8)

extract_protocol:
Omni-ATAC-seq sample preparation was performed as previously described. After flow cytometric sorting, 50,000 cells were lysed with 50 µl cold ATAC-Resuspension buffer (RSB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20) with 0.1% NP40, and 0.01% Digitonin on ice for 3 min. Lysis was stopped with 1 mL cold ATAC-RSB.
After centrifugation (500×g for 10 min), nuclei were resuspended in 50μl transposition reaction containing 2.5μl Tn5 transposase (FC-121–1030; Illumina) to tag and fragmentalize accessible chromatin. The reaction was incubated at 37°C, 400rpm for 30 min; DNA was then purified using a MinElute kit (QIAGEN) and amplified with 8–12 cycles of PCR based on the amplification curve. Samples were purified using a MinElute kit, sequenced on a NovaSeq 6000, paired end, 50 cycles

treatment_protocol: Human peripheral blood mononuclear cells (PBMC) were isolated by density centrifugation (Ficoll-Paque). Naïve human CD4+ T cells were magnetically enriched to >95% purity (StemCell) and plated at a density of 0.5 x10^6  on plate-bound aCD3 (1 μg/mL, OKT3), in the presence of cytokines and antibodies to promote the differentiation of Th1 (1 μg/mL aCD28, 2.5 μg/mL aIFN-γ, 2.5 μg/mLaIL-10, 30ng/mL hIL-4, 10 ng/mL hIL-2). After 5 days, cells were washed and cultured without aCD3 or aCD28 but with all polarizing cytokines and antibodies for an additional 3 days (media, cytokines, and antibodies changed every 2 days, total 8 days of culture)

value: In vitro differentiated Th1 (d8)


title: 4167_Naive_K27Ac_S28


title: Naïve Old E1

description: RNA was isolated from 5 mice


title: Naïve Old E9

description: RNA was isolated from 5 mice


title: Naïve Old E2

description: RNA was isolated from 5 mice


title: 4167_d15_K4me3_S9

value: In vitro differentiated Th9 (d15)


title: 3340_Th1


title: 3dps_IL12_73_S28

description:
3dps_Raw_gene_counts_matrix.tsv
All_DEGs_3dps+IL12_KO vs WT.xlsx
All_DEGs_WT _3dps+IL12 vs 3dps.xlsx
All_DEGs_KO_3dps+IL12 vs 3dps.xlsx

source_name: CD8+ T cells

growth_protocol: Magnetic associated cell sorting (MACS) -isolated naive CD8+ T cells from spleen and lymph nodes were grown in 1ml of X-VIVO™ 20 Serum-free Hematopoietic Cell Medium (Lonza) at 37°C for 3 days.

extract_protocol:
Culture plates were placed on ice for the extraction procedure. Cells were washed with 1ml of cold 1xPBS, suspended in 350µl of RLT-plus lysis buffer (Qiagen) and the total RNA was exctracted using RNEasy Plus Mini Kit (Qiagen).
NEBNext Ultra II Directional RNA library after polyA purification

treatment_protocol: Cells were stimulated during growth using plate-bound anti-CD3 (17A2; 5µg/ml, eBioscience/Thermo Fisher Scientific) and anti-CD28 antibodies (37.51; 5µg/ml, eBioscience/Thermo Fisher Scientific) without added cytokines or in the presence of recombinant IL12 (10ng/ml) (Peprotech, New Jersey, USA) or TGFB1 (0.5ng/ml) (Peprotech).

tag: background

value: 8 weeks

value: Furin KO

value: Anti-CD3 and anti-CD28 stimulation + recombinant IL12


title: 3dps_IL12_75_S30

value: WT


title: 3dps_IL12_74_S29


title: 3dps_IL12_72_S27


title: d15_4031_ATAC_S4


title: 3dps_IL12_71_S26


title: Naïve Old D12

description: RNA was isolated from 5 mice

value: Lymphatic endothelial cells


title: Naïve Old D11

description: RNA was isolated from 5 mice

value: female


title: Naïve Old D10

description: RNA was isolated from 5 mice

value: Spinal cord meninges


title: 3dps_IL12_70_S25


title: Naïve Old D9

description: RNA was isolated from 5 mice

value: Naïve


title: Grn-/-; GRNtg mouse 1

value: Cortex

value: male

value: 18 months


title: d8_4031_ATAC_S3

value: In vitro differentiated Th9 (d8)


title: 3dps_IL12_67_S23


title: d15_4028_ATAC_S10


title: d8_4028_ATAC_S9


title: 3dps_IL12_68_S24


title: d5_4031_ATAC_S2

treatment_protocol: Human peripheral blood mononuclear cells (PBMC) were isolated by density centrifugation (Ficoll-Paque). Naïve human CD4+ T cells were magnetically enriched to >95% purity (StemCell) and plated at a density of 1 x10^6 on plate-bound aCD3 (1 μg/mL, OKT3), in the presence of cytokines and antibodies to promote the differentiation of Th9 (1 μg/mL aCD28, 2.5 μg/mL aIFN-γ, 5 ng/mL hTGFβ, 10 ng/mL hIL-2, 30 ng/mL hIL-4, 10 ng/mL hIL-1β).

value: In vitro differentiated Th9 (d5)


title: Naïve Old D8

description: RNA was isolated from 5 mice


title: Naïve Old D7

description: RNA was isolated from 5 mice


title: 3dps_IL12_63_S22


title: 3dps_IL12_62_S21


title: d5_4028_ATAC_S8


title: Naïve Old D6

description: RNA was isolated from 5 mice


title: 3dps_Tgfb1_75_S20

description:
3dps_Raw_gene_counts_matrix.tsv
All_DEGs_3dps+TGFB1_KO vs WT.xlsx
All_DEGs_WT_3dps+TGFB1 vs 3dps.xlsx
All_DEGs_KO_3dps+TGFB1 vs 3dps.xlsx

value: Anti-CD3 and anti-CD28 stimulation + recombinant TGFB1


title: 3dps_Tgfb1_74_S19


title: Naïve Old D4

description: RNA was isolated from 5 mice

value: 24 months


title: naive_4028_ATAC_S7

value: naive T cells


title: G3BP_KO_G3BP1_rescue_RNA-Seq_rep1

description:
G3BP_KO_DESeq2_results_KO_vs_G3BP1_rescue.tabular
G3BP_KO_DESeq2_results_KO_vs_WT.tabular

data_processing:
Alignment with STAR (v.2.7.0f)
Nucleotide frequency at each position in the transcriptome was uploaded to MySQL database.
A-to-I mutations were detected by comparing the nucleotide frequencies in each sample with the background control.
Differential expression with DESeq2 (v.2.11.40.6)
Assembly: CRCh38
Supplementary files format and content: For bedgraph files, first three columns denote genomic coordinates of edit sites. The fourth column represents the editing percentages of edit sites.
Supplementary files format and content: Tabular files are output of DESeq2.

value: Bone osteosarcoma epithelial cells

value: G3BP1/2 knockout

value: Transient transfection

value: Lipofectamine transfection of G3BP1 transgene

value: 24 hour post-transfection


title: 3dps_Tgfb1_73_S18

value: 8 weeks

value: Furin KO


title: 3dps_Tgfb1_72_S17

value: WT

value: female


title: Naïve Old D5

description: RNA was isolated from 5 mice

value: Spinal cord meninges

value: Lymphatic endothelial cells

value: Naïve


title: Naïve Old D2

description: RNA was isolated from 5 mice


title: Naïve Old D1

description: RNA was isolated from 5 mice


title: G3BP_WT_RNA-Seq_rep2


title: Naïve Old D3

description: RNA was isolated from 5 mice


title: 3dps_Tgfb1_71_S16


title: Naïve Old C12

description: RNA was isolated from 5 mice


title: G3BP_WT_RNA-Seq_rep1


title: G3BP_KO_RNA-Seq_rep2


title: 3dps_Tgfb1_70_S15


title: Naïve Old C11

description: RNA was isolated from 5 mice


title: G3BP_KO_RNA-Seq_rep1


title: 3dps_Tgfb1_68_S14


title: Naïve Old C9

description: RNA was isolated from 5 mice


title: 3dps_Tgfb1_67_S13


title: G3BP1_input_RIP-Seq_rep2

description: G3BP1_RIP-Seq_DESeq2_results_IP_vs_input.tabular

value: FlpIn 293 Trex

value: Embryonic kidney cells

value: Stable expression of FLAG-G3BP1

value: Tetracycline induction

value: 1ug/mL tetracycline

value: 24 hour for tetracycline


title: naive_4031_ATAC_S1

value: naive T cells


title: Naïve Old C10

description: RNA was isolated from 5 mice

value: 24 months


title: 3dps_Tgfb1_62_S11

value: male

value: Anti-CD3 and anti-CD28 stimulation + recombinant TGFB1


title: G3BP1_input_RIP-Seq_rep3


title: Naïve Old C8

description: RNA was isolated from 5 mice


title: G3BP_KO_G3BP1_rescue_RNA-Seq_rep2

value: Bone osteosarcoma epithelial cells

value: G3BP1/2 knockout

value: Transient transfection

value: Lipofectamine transfection of G3BP1 transgene

value: 24 hour post-transfection


title: G3BP1_IP_RIP-Seq_rep3


title: G3BP1_input_RIP-Seq_rep1


title: Naïve Old C7

description: RNA was isolated from 5 mice

value: Spinal cord meninges

value: Lymphatic endothelial cells

value: female


title: 3dps_75_S10

description:
3dps_Raw_gene_counts_matrix.tsv
All_DEGs_3dps_KO vs WT.xlsx
All_DEGs_WT_3dps+TGFB1 vs 3dps.xlsx
All_DEGs_WT _3dps+IL12 vs 3dps.xlsx
All_DEGs_KO_3dps+TGFB1 vs 3dps.xlsx
All_DEGs_KO_3dps+IL12 vs 3dps.xlsx

value: 8 weeks

value: WT

value: Only anti-CD3 and anti-CD28 stimulation


title: G3BP1_IP_RIP-Seq_rep2

value: FlpIn 293 Trex

value: Embryonic kidney cells

value: Stable expression of FLAG-G3BP1

value: Tetracycline induction

value: 1ug/mL tetracycline


title: 3dps_73_S8

value: Furin KO


title: G3BP1_IP_RIP-Seq_rep1

value: 24 hour for tetracycline


title: 3dps_74_S9


title: Naïve Old C5

description: RNA was isolated from 5 mice

value: 24 months

value: Naïve


title: Naïve Old C4

description: RNA was isolated from 5 mice


title: TRIBE-ID_inhibitors_no_treament_rep2

value: Stable expression of G3BP1-FRB and FKBP-ADAR


title: 3dps_72_S7


title: 3dps_71_S6


title: Naïve Old C3

description: RNA was isolated from 5 mice


title: 3dps_Tgfb1_63_S12

value: male

value: Anti-CD3 and anti-CD28 stimulation + recombinant TGFB1


title: TRIBE-ID_inhibitors_no_treament_rep1


title: Naïve Old C2

description: RNA was isolated from 5 mice

value: Spinal cord meninges

value: Lymphatic endothelial cells


title: 3dps_70_S5

value: 8 weeks

value: female


title: Naïve Old C1

description: RNA was isolated from 5 mice


title: 3dps_67_S3

value: WT

value: Only anti-CD3 and anti-CD28 stimulation


title: TRIBE-ID_inhibitors_EGCG_rep2

value: FlpIn 293 Trex

value: Embryonic kidney cells

value: Tetracycline induction, rapamycin and EGCG treatment

value: 1ug/mL tetracycline, 100 nM rapamycin, 20 uM EGCG

value: 24 hour for tetracycline, 2 hour for rapamycin and EGCG


title: TRIBE-ID_inhibitors_rapamycin-only_rep1

value: Tetracycline induction, rapamycin treatment

value: 1ug/mL tetracycline, 100 nM rapamycin

value: 24 hour for tetracycline, 2 hour for rapamycin


title: Naïve Old B11

description: RNA was isolated from 5 mice

value: 24 months

value: Naïve


title: 3dps_63_S2

value: Furin KO

value: male


title: Naïve Old C6

description: RNA was isolated from 5 mice

value: Spinal cord meninges

value: Lymphatic endothelial cells


title: Naïve Old B10

description: RNA was isolated from 5 mice

value: female


title: 3dps_62_S1

value: 8 weeks

value: WT


title: Naïve Old B8

description: RNA was isolated from 5 mice


title: TRIBE-ID_inhibitors_RSVL_rep2

value: FlpIn 293 Trex

value: Stable expression of G3BP1-FRB and FKBP-ADAR

value: Tetracycline induction, rapamycin and RSVL treatment

value: 1ug/mL tetracycline, 100 nM rapamycin, 20 uM RSVL

value: 24 hour for tetracycline, 2 hour for rapamycin and RSVL


title: TRIBE-ID_inhibitors_EGCG_rep1

value: Embryonic kidney cells

value: Tetracycline induction, rapamycin and EGCG treatment

value: 1ug/mL tetracycline, 100 nM rapamycin, 20 uM EGCG

value: 24 hour for tetracycline, 2 hour for rapamycin and EGCG


title: TRIBE-ID_inhibitors_RSVL_rep1


title: Naïve Old B9

description: RNA was isolated from 5 mice

value: 24 months

value: Naïve


title: TRIBE-ID_inhibitors_PDS_rep2

value: Tetracycline induction, rapamycin and PDS treatment

value: 1ug/mL tetracycline, 100 nM rapamycin, 20 uM PDS

value: 24 hour for tetracycline, 2 hour for rapamycin and PDS


title: Naïve Old B7

description: RNA was isolated from 5 mice

value: Spinal cord meninges

value: Lymphatic endothelial cells

value: female


title: 3dps_68_S4

value: 8 weeks

value: Furin KO

value: Only anti-CD3 and anti-CD28 stimulation


title: Naïve Old B12

description: RNA was isolated from 5 mice


title: Naïve Old B5

description: RNA was isolated from 5 mice


title: TRIBE-ID_4hr_rapamycin_NaAsO2_rep1

value: FlpIn 293 Trex

value: Stable expression of G3BP1-FRB and FKBP-ADAR

value: Tetracycline induction, rapamycin and sodium arsenite treatment

value: 1ug/mL tetracycline, 100 nM rapamycin, 200 uM sodium arsenite

value: 24 hour for tetracycline, 4 hour for rapamycin and sodium arsenite


title: TRIBE-ID_inhibitors_rapamycin-only_rep2

value: Embryonic kidney cells

value: Tetracycline induction, rapamycin treatment

value: 1ug/mL tetracycline, 100 nM rapamycin

value: 24 hour for tetracycline, 2 hour for rapamycin