title: S044 [204425710094_R03C01]

value: male

value: Mesothelioma, biphasic


title: S045 [204425710094_R06C01]

status: Public on May 17 2022

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

country: Germany

institute: Ludwig Maximilians University Hospital Munich

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
Statistical analysis was performed using the minfi package running on RStudio version 1.4.1717 based on the statistical language R version 4.1.1
The 'bVals_matrix.csv' contains average beta-Values after normalization using the Noob method

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: specimen

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

tag: gender

tag: age

tag: diagnosis


title: BA treatment 12hpi infecting rep3

type: SRA

city: UPPSALA

first: Anna

last: Kokla

state: Select

address: Biocenter, Almas allé 5

department: Plant Biology

country: Sweden

institute: SLU

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
BA_12_I_3

library_source: transcriptomic

data_processing:
adapter and low-quality sequences were removed using the fastp software
The quality-filtered reads were mapped to both the Phtheirospermum  and Arabidopsis genome (TAIR10) using STAR and were separated based on mapping to Phtheirospermum and Arabidopsis reads.The separated reads were then re-mapped to their respective genomes.
The raw read count was calculated using FeatureCounts
The differential expression analysis was performed using Deseq2
Genome_build: Pjv1 for Phtheirospermum and TAIR 10 for Arabidopsis
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism:
Arabidopsis thaliana
Phtheirospermum japonicum

source_name: Root

growth_protocol: Phtheirospermum and Arabidopsis seeds were surface sterilized with ethanol, plated on 1/2MS+1%sucroze+0.8%plantagar plates and stratified for 2 days. Seedlings were grown for 4 days in long day conditions, 16h light (25 C) and 8h darkness (25 C) at light intensity of 100µE/m2/s.

extract_protocol:
Total RNA was extracted using the ROTI®Prep RNA MINI (Roth) kit
RNA libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® for paired end sequencing

treatment_protocol: Phtheirospermum seedlings were transferred to 0.8% plant agar plates containing DMSO or 10.3mM ammonium nitrate or 80nM 6-Benzylaminopurine for 3 days prior to the Arabidopsis addition (infecting samples). Arabidopsis and Phtheirospermum were transferes in the same treatments but separetely for the not infecting samples. 40 plants were used per sample. The 2mm root tip (0hpi samples and not infecting samples) or the haustorium formation site +/- 2mm above and below were harvested (infecting samples) for both Phtheirospermum and Arabidopsis.

tag: genotype

value: Phtheirospermum Okayama anr Arabidopsis Col-56

tag: tissue

value: root tissue including the haustorium formation site and 1-2 mm above and below it

tag: treatment

tag: time

value: Arabidopsis at 12hpi


title: RA_1002

city: Chicago

first: Igor

last: Efimov

state: Illinois

address: 303 E Superior St

country: USA

institute: Northwestern University

data_processing:
Sequencing adapters were removed with trimmomatic v0.39 and low-quality reads were filtered with the tool’s default settings (leading:3, trailing:3, slidingwindow:4:15).
Filtered reads were aligned with kallisto v0.48.0 to Rattus norvegicus genome release 105 (http://ftp.ensembl.org/pub/release-105/fasta/rattus_norvegicus/cdna/).
Expression values were calculated with tximport v1.22.0
Assembly: Rattus norvegicus genome release 105
Supplementary files format and content: Matrix with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix with raw transcript counts for every sample
Supplementary files format and content: Matrix witnormlized gene counts (tpm) for every gene and every sample
Supplementary files format and content: Matrix with raw transcript counts (tpm) for every\every sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat heart

growth_protocol: 1-week-old male Sprague-Dawley rat pups underwent an ascending aortic constriction that led to the development of left ventricular hypertrophy by 10 weeks of age.

extract_protocol:
Explanted rat hearts were arrested with the cardioplegic solution. Tissues (~5mg) were collected from inferior and superior sinoatrial nodefrom the left and right atria,  and left ventricles. The tissue was stored in RNAlater (Invitrogen) overnight at +4 °C and  stored at -80 °C. Total mRNA was extracted with RNeasy Micro Kit (Qiagen). RNA purity and yield were quality checked with Agilent Bioanalyzer to satisfy RIN >7 and total RNA amount 3-5 μg.
TruSeq RNA Library Prep Kit (Illumina)

tag: cardiac chamber

value: Right atrium

tag: Sex

value: Male

value: 10 weeks

tag: health state

value: healthy

tag: strain

value: Sprague-Dawley rat


title: SmA3_NPC_d21_Rep1

city: Oxford

first: Joseph

middle: S

last: Bowness

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description:
SmA3_NPC_d21_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

data_processing:
The standard ChrRNA-seq data mapping pipeline is reported in our previous study (Nesterova et al., 2019). Briefly, raw fastq files of read pairs were first mapped to rRNA by bowtie2 (v2.3.2; Langmead and Salzberg 2012) and rRNA-mapping reads discarded (typically <2%). The remaining unmapped reads were aligned to an N-masked mm10 genome with STAR (v2.4.2a; Dobin et al., 2013) using parameters: “-outFilterMultimapNmax 1 -outFilterMismatchNmax 4 -alignEndsType EndToEnd”.
Aligned reads were assigned to separate files for either the Cast or Dom/129S genomes by SNPsplit (v0.2.0; Krueger and Andrews, 2016) using the “- paired” parameter and a SNPfile containing the 23,005,850 SNPs between Cast and Dom/129S genomes (UCSC).
Read fragments overlapping genes, for both the ‘unsplit’ and ‘allelic’ files of each sample, were counted by the program featureCounts (Liao et al., 2014) using an annotation file of all transcripts and lncRNAs from NCBI RefSeq and the parameters “-t transcript -g gene id -s 2”.
Further allelic analysis was performed using R and RStudio on allelic count matrix output files from featureCounts. X-linked genes with at least 10 allelically-assigned fragments (i.e. containing reads that overlap SNPs) in >80% of WT samples were retained for gene silencing analysis. Gene silencing was assessed by calculating the allelic ratio of read counts, given by Xi/(Xi + Xa). An additional filter on the allelic ratio in uninduced mESCs (0.1 < allelic ratio < 0.9) was also applied, as strongly monoallelic genes are likely to be technical artifacts of singular mis-annotated SNPs.
Genome_build: mm10
Supplementary_files_format_and_content: counts tables, allelic ratio

organism: Mus musculus

source_name: iXist-ChrX-Dom(mESC)

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged and colleced with TrypLE (ThermoFisher) and frozen in FCS + 10% DMSO. Mitomycin C-inactivated mouse fibroblasts were used as feeders and removed prior to plating out for experiments by pre-plating. For NPC differentiation timepoints, mESCs were first extensively separated from feeder cells by pre-plating four times for 35-40 min each. 0.5 x 106 mESCs were then plated to gelatin-coated T25 flasks and grown in N2B27 media (50:50 DMEM/F-12:Neurobasal (Gibco) supplemented with 1 X N2 and 1 X B27 (ThermoFisher), 1 mM L-glutamine, 100 μM β-mercaptoethanol, 50 U/mL penicillin / 50 μg/mL streptomycin (all from Life Technologies) with 1 μg/mL doxycycline for continuous Xist induction.

extract_protocol:
Between 5 x 106 (NPC) and 3 x 107 (mESC) cells were collected from confluent 90mm dishes, washed once with PBS, then snap-frozen and stored at -80oC. Chromatin extraction was performed as follows: Cell pellets were lysed on ice for 5 min in RLB (10 mM Tris pH7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40). Nuclei were then purified by centrifugation through 24% sucrose/RLB (2800 g for 10 min at 4oC), resuspended in NUN1 (20 mM Tris pH7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.1 mM DTT), and then lysed by gradual addition of an equal volume NUN2 (20 mM HEPES pH 7.9, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea, 0.1 mM DTT). After 15 min incubation on ice with occasional vortexing, the chromatin fraction was isolated as the insoluble pellet after centrifugation (2800 g for 10 min at 4oC). Chromatin pellets were resuspended in 1mL TRIzol (Invitrogen) and fully homogenenized and solubilized by eventually being passed through a 23-gauge needle 10 times . This was followed by isolation of chromatin-associated RNA through TRIzol/chloroform extraction with isopropanol precipitation. Precipitated RNA pellets were washed twice with 70% ethanol. Final ChrRNA samples were then resuspended in H2O, treated with TurboDNAse and measured by Nanodrop (both ThermoFisher). 500 ng – 1 µg of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit (RS-122-2301).
Illumina TruSeq stranded total RNA kit (500 ng – 1 µg of RNA)

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1μg/mL) to the culture medium for 1, 3 or 6 days. For FKBP12-PCGF35 lines, dTAG-13 was added at 100uM 12 hours prior to Dox inductiom.

value: Dom/129S x Cast

tag: cell type

value: NPC

value: Female

tag: cell engineering

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); SmcHD1 KO

tag: xist (dox) induction time

value: 21 days


title: RA_1001


title: BA treatment 12hpi not infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
BA_12_U_1

value: Phtheirospermum Okayama anr Arabidopsis Col-57


title: SmA3_NPC_d2_Rep1

description:
SmA3_NPC_d2_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: mESC to NPC

value: 2 days


title: S043 [204425700081_R08C01]

value: male

value: Mesothelioma, sarcomatoid


title: SB_0920

value: Inferior sino-atrial node


title: RA_0920


title: S040 [204425700081_R02C01]

value: female

value: Mesothelioma, epitheloid


title: SmA3_NPC_d15_Rep2

description:
SmA3_NPC_d15_Rep2
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: 15 days


title: RA_0508

value: Right atrium

value: Male

value: 10 weeks

value: failing


title: S041 [204425700081_R04C01]

value: Lung adenocarcinoma, pleural carcinosis


title: BA treatment 12hpi infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
BA_12_I_2

value: Phtheirospermum Okayama anr Arabidopsis Col-55

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Arabidopsis at 12hpi


title: SmA3_ES_Rep2

description:
SmA3_ES_Rep2
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: Dom/129S x Cast

value: mESC

value: Female

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); SmcHD1 KO


title: RA_0507

value: Sprague-Dawley rat


title: iXist-ChrX-Cast_NPC_d7_Rep3

description:
C7H8_NPC_d7_Rep3
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

source_name: iXist-ChrX-Cast(mESC)

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (Cast allele)

value: 7 days


title: BA treatment 0hpi not infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
BA_0_U_1

value: Phtheirospermum Okayama anr Arabidopsis Col-51

value: Arabidopsis at 0hpi


title: BA treatment 0hpi not infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
BA_0_U_2

value: Phtheirospermum Okayama anr Arabidopsis Col-52


title: S038 [204425700079_R08C01]

value: male

value: Mesothelioma, sarcomatoid


title: BA treatment 0hpi not infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
BA_0_U_3

value: Phtheirospermum Okayama anr Arabidopsis Col-53


title: S039 [204425700081_R01C01]

value: female

value: Pleomorphic lung carcinoma, lung adenocarcinoma with >10% spindle cells


title: RA_0921

value: Right atrium

value: Male

value: 10 weeks

value: healthy


title: SmA3_ES_Rep1

description:
SmA3_ES_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: Dom/129S x Cast

value: mESC

value: Female

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); SmcHD1 KO


title: iXist-ChrX-Cast_NPC_d7_Rep1

description:
C7H8_NPC_d7_Rep1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (Cast allele)

value: 7 days


title: RA_0506

value: failing

value: Sprague-Dawley rat


title: BA treatment 0hpi infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
BA_0_I_2

value: Phtheirospermum Okayama anr Arabidopsis Col-49

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Arabidopsis at 0hpi


title: S042 [204425700081_R05C01]

value: female

value: Pleomorphic lung carcinoma, lung adenocarcinoma with >10% spindle cells


title: iXist-ChrX-Cast_NPC_d7_Rep2

description:
C7H8_NPC_d7_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: BA treatment 12hpi infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
BA_12_I_1

value: Phtheirospermum Okayama anr Arabidopsis Col-54

value: Arabidopsis at 12hpi


title: BA treatment 0hpi infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
BA_0_I_3

value: Phtheirospermum Okayama anr Arabidopsis Col-50


title: S035 [204425700079_R04C01]

value: Lung adenocarcinoma, pleural carcinosis


title: S036 [204425700079_R06C01]


title: BA treatment 0hpi infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
BA_0_I_1

value: Phtheirospermum Okayama anr Arabidopsis Col-48


title: iXist-ChrX-Cast_NPC_d5_Rep3

description:
C7H8_NPC_d5_Rep3
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Dom/129S x Cast

value: Female

value: 5 days


title: iXist-ChrX-Cast_NPC_d5_Rep1

description:
C7H8_NPC_d5_Rep1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (Cast allele)


title: LV_1001

value: Left ventricle

value: Male

value: 10 weeks

value: healthy


title: iXist-ChrX-Cast_NPC_d5_Rep2

description:
C7H8_NPC_d5_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: N treatment 24hpi not infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
N_24_U_3

value: Phtheirospermum Okayama anr Arabidopsis Col-47

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Ammonium nitrate

value: Arabidopsis at 24hpi


title: N treatment 24hpi not infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
N_24_U_2

value: Phtheirospermum Okayama anr Arabidopsis Col-46


title: S033 [204425700079_R02C01]

value: male

value: Mesothelioma, epitheloid


title: S034 [204425700079_R03C01]

value: Pleomorphic lung carcinoma, lung adenocarcinoma with >10% spindle cells


title: LV_1002

value: Sprague-Dawley rat


title: S037 [204425700079_R07C01]


title: N treatment 24hpi not infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
N_24_U_1

value: Phtheirospermum Okayama anr Arabidopsis Col-45


title: iXist-ChrX-Cast_NPC_d3_Rep2

description:
C7H8_NPC_d3_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Dom/129S x Cast

value: Female

value: 3 days


title: iXist-ChrX-Cast_NPC_d3_Rep3

description:
C7H8_NPC_d3_Rep3
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (Cast allele)


title: N treatment 24hpi infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
N_24_I_3

value: Phtheirospermum Okayama anr Arabidopsis Col-44


title: iXist-ChrX-Cast_NPC_d3_Rep1

description:
C7H8_NPC_d3_Rep1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: LV_0507

value: Left ventricle

value: Male

value: 10 weeks

value: failing


title: S030 [204425700076_R04C01]

value: female

value: Lung adenocarcinoma, pleural carcinosis


title: LA_1002

value: Left atrium

value: healthy


title: iXist-ChrX-Cast_NPC_d35

description:
C7H8_NPC_d35
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: NPC

value: 35 days


title: RA_0409

value: Right atrium

value: Sprague-Dawley rat


title: S032 [204425700076_R06C01]

value: male


title: LV_0506


title: N treatment 12hpi not infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
N_12_U_3

value: Phtheirospermum Okayama anr Arabidopsis Col-41

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Ammonium nitrate

value: Arabidopsis at 12hpi


title: LA_1001


title: LV_0508

value: Left ventricle


title: LV_0409

value: Male


title: S028 [204425700076_R01C01]


title: N treatment 24hpi infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
N_24_I_2

value: Phtheirospermum Okayama anr Arabidopsis Col-43

value: Arabidopsis at 24hpi


title: N treatment 24hpi infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
N_24_I_1

value: Phtheirospermum Okayama anr Arabidopsis Col-42


title: iXist-ChrX-Cast_NPC_d2_Rep1

description:
C7H8_NPC_d2_Rep1
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Dom/129S x Cast

value: mESC to NPC

value: Female

value: Endogenous Xist promoter replaced with TetOn Promoter (Cast allele)

value: 2 days


title: LA_0921

value: Left atrium

value: 10 weeks

value: healthy


title: S029 [204425700076_R02C01]

value: male

value: Mesothelioma, epitheloid


title: S027 [204425700012_R08C01]

value: Mesothelioma, sarcomatoid


title: N treatment 12hpi not infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
N_12_U_2

value: Phtheirospermum Okayama anr Arabidopsis Col-40

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Ammonium nitrate

value: Arabidopsis at 12hpi


title: iXist-ChrX-Cast_NPC_d2_Rep2

description:
C7H8_NPC_d2_Rep2
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt


title: iXist-ChrX-Cast_NPC_d15

description:
C7H8_NPC_d15
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: NPC

value: 15 days


title: iXist-ChrX-Cast_NPC_d21

description:
C7H8_NPC_d21
WTvSmcHD1_iXist-ChrX-Cast_AllelicRatio_table.txt

value: Dom/129S x Cast

value: 21 days


title: LA_0508

value: Male

value: failing

value: Sprague-Dawley rat


title: S025 [204425700012_R06C01]


title: S031 [204425700076_R05C01]

value: Pleomorphic lung carcinoma, lung adenocarcinoma with >10% spindle cells


title: LA_0920

value: Left atrium

value: 10 weeks


title: S026 [204425700012_R07C01]

value: female


title: iXist-ChrX-Dom_NPC_d7_Rep2

description:
A11B2_NPC_d7_Rep2
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: mESC to NPC

value: Female

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele)

value: 7 days


title: N treatment 12hpi infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
N_12_I_3

value: Phtheirospermum Okayama anr Arabidopsis Col-38

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Ammonium nitrate


title: LA_0506


title: LA_0507


title: N treatment 12hpi infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
N_12_I_2

value: Phtheirospermum Okayama anr Arabidopsis Col-37

value: Arabidopsis at 12hpi


title: iXist-ChrX-Dom_NPC_d7_Rep1

description:
A11B2_NPC_d7_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: Dom/129S x Cast


title: N treatment 12hpi infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
N_12_I_1

value: Phtheirospermum Okayama anr Arabidopsis Col-36


title: S022 [204425700012_R03C01]


title: S024 [204425700012_R05C01]

value: male


title: iXist-ChrX-Dom_NPC_d5_Rep2

description:
A11B2_NPC_d5_Rep2
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: 5 days


title: N treatment 12hpi not infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
N_12_U_1

value: Phtheirospermum Okayama anr Arabidopsis Col-39


title: S021 [204425700012_R02C01]

value: Mesothelioma, epitheloid


title: iXist-ChrX-Dom_NPC_d5_Rep1

description:
A11B2_NPC_d5_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt


title: N treatment 0hpi not infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
N_0_U_3

value: Phtheirospermum Okayama anr Arabidopsis Col-35

value: Arabidopsis at 0hpi


title: iXist-ChrX-Dom_NPC_d3_Rep2

description:
A11B2_NPC_d3_Rep2
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: mESC to NPC

value: 3 days


title: iXist-ChrX-Dom_NPC_d52

description:
A11B2_NPC_d52
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: NPC

value: Female

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele)

value: 52 days


title: N treatment 0hpi not infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
N_0_U_1

value: Phtheirospermum Okayama anr Arabidopsis Col-33

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Ammonium nitrate


title: N treatment 0hpi not infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
N_0_U_2

value: Phtheirospermum Okayama anr Arabidopsis Col-34


title: N treatment 0hpi infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
N_0_I_3

value: Phtheirospermum Okayama anr Arabidopsis Col-32


title: S020 [204390590126_R08C01]

value: female


title: iXist-ChrX-Dom_NPC_d3_Rep1

description:
A11B2_NPC_d3_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: Dom/129S x Cast


title: S019 [204390590126_R07C01]

value: male

value: Pleomorphic lung carcinoma, lung squamous cell carcinoma with >10% spindle cells


title: iSAN0506

value: Inferior sino-atrial node

value: Male

value: 10 weeks

value: failing

value: Sprague-Dawley rat


title: iSAN0409


title: S023 [204425700012_R04C01]

value: Lung adenocarcinoma, pleural carcinosis


title: N treatment 0hpi infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
N_0_I_2

value: Phtheirospermum Okayama anr Arabidopsis Col-31

value: Arabidopsis at 0hpi


title: S018 [204390590124_R08C01]

value: Mesothelioma, epitheloid


title: N treatment 0hpi infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
N_0_I_1

value: Phtheirospermum Okayama anr Arabidopsis Col-30

value: root tissue including the haustorium formation site and 1-2 mm above and below it


title: LA_0409

value: Left atrium


title: S017 [204390590124_R02C01]


title: iXist-ChrX-Dom_NPC_d2_Rep2

description:
A11B2_NPC_d2_Rep2
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: mESC to NPC

value: Female

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele)

value: 2 days


title: Day7 Nontarget no input, ChIP-seq

city: La Jolla

first: John

last: Chang

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: UC San Diego

description: ChIP-seq Libraries

library_source: genomic

data_processing:
Libraries were filtered and mapped to the mm10 genome using ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline with default parameters for histone marks (github.com/ENCODE-DCC/chip-seq-pipeline2). Final pooled bigwig files were used for visualization.
none provided by the submitter
Assembly: mm10
Supplementary files format and content: bigwig files from pooled replicates

source_name: Spleen

extract_protocol:
Spleens from P14 mice were homogenized, and 1x106 cells/mL in TCM were pulsed with 1 ng/ml LCMV GP33–41 peptide for 1 hour at 37°C. Cells were washed once with equal volume of warm TCM, then plated in a 96 well-plate at 5x104 cells/well. Cells were harvested 4.5 days later and dead cells removed using the Dead Cell Removal kit according to the manufacturer’s protocol (Miltenyi Biotec, Catalog number: 130-010-101). CD8+ T cells were then enriched using the CD8a+ T Cell Isolation Kit.
Chromatin was then prepared using the EMD Millipore Magna ChIP A/G Chromatin Immunoprecipitation Kit according to manufactures protocol (Catalog Number: 1710085) and flash frozen in liquid nitrogen. Nuclei were sheared in Covaris microTUBES (Catalog number: 520045) using the Covaris E220 (Peak Incident Power 175W, Duty Factor 10%, Cycles per Burst 200, Treatment Time 600 seconds). For each immunoprecipitation (IP), 3 mg antibody per 1e6 cell equivalents were used for overnight incubation at 4°C. Antibodies used for IPs were as follows: anti-H3K27me3 (07-449, EMD Millipore), anti-H3K4me3 (ab8580, abcam). and anti-Ezh2 (AC22, 07-449, EMD Millipore). Five percent of each sample was kept as input control.

value: CD8 T cells

value: Spleen

value: 6-8 weeks old


title: iSAN0508

value: Inferior sino-atrial node

value: Male

value: 10 weeks


title: iSAN0507

value: failing

value: Sprague-Dawley rat


title: Day7 Malat1 Knockdown no input, ChIP-seq

description: ChIP-seq Libraries


title: Day7 H3K4me3 Nontarget Knockdown, replicate 2, ChIP-seq

description: ChIP-seq Libraries


title: DMSO treatment 72hpi not infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 72hpi
DMSO_72_U_3

value: Phtheirospermum Okayama anr Arabidopsis Col-29

value: DMSO control

value: Arabidopsis at 72hpi


title: S015 [204361730144_R01C01]

value: male

value: Pleomorphic lung carcinoma, lung adenocarcinoma with >10% spindle cells


title: Day7 H3K4me3 Nontarget Knockdown, replicate 1, ChIP-seq

description: ChIP-seq Libraries


title: DMSO treatment 72hpi not infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 72hpi
DMSO_72_U_2

value: Phtheirospermum Okayama anr Arabidopsis Col-28

value: root tissue including the haustorium formation site and 1-2 mm above and below it


title: iXist-ChrX-Dom_NPC_d21

description:
A11B2_NPC_d21
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: Dom/129S x Cast

value: NPC

value: Female

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele)

value: 21 days


title: DMSO treatment 72hpi infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 72hpi
DMSO_72_I_3

value: Phtheirospermum Okayama anr Arabidopsis Col-26


title: S016 [204390590106_R03C01]

value: female

value: Pleomorphic lung carcinoma, lung squamous cell carcinoma with >10% spindle cells


title: DMSO treatment 72hpi not infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 72hpi
DMSO_72_U_1

value: Phtheirospermum Okayama anr Arabidopsis Col-27


title: iXist-ChrX-Dom_NPC_d15

description:
A11B2_NPC_d15
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: 15 days


title: S013 [204339300065_R01C01]


title: S014 [204361730143_R01C01]


title: iXist-ChrX-Dom_NPC_d35

description:
A11B2_NPC_d35
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: 35 days


title: SpocH1_NPC_d6

description:
SpocH1_NPC_d6
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); mutation of Spen SPOC domain

value: 6 days

tag: dtag-13 treatment


title: S012 [204339110053_R03C01]

value: Mesothelioma, epitheloid


title: DMSO treatment 72hpi infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 72hpi
DMSO_72_I_2

value: Phtheirospermum Okayama anr Arabidopsis Col-25

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: DMSO control

value: Arabidopsis at 72hpi


title: S011 [204339110049_R06C01]

value: male


title: Day7 H3K27me3 Nontarget Knockdown, replicate 2, ChIP-seq

description: ChIP-seq Libraries

value: CD8 T cells

value: Spleen

value: 6-8 weeks old


title: DMSO treatment 72hpi infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 72hpi
DMSO_72_I_1

value: Phtheirospermum Okayama anr Arabidopsis Col-24


title: SpocH1_NPC_d3

description:
SpocH1_NPC_d3
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: Female

value: 3 days


title: iXist-ChrX-Dom_NPC_d2_Rep1

description:
A11B2_NPC_d2_Rep1
WTvSmcHD1_iXist-ChrX-Dom_AllelicRatio_table.txt

value: Dom/129S x Cast

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele)

value: 2 days


title: SpocH1_ES_d1

description:
SpocH1_ES_d1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: mESC

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); mutation of Spen SPOC domain

value: 1 day


title: DMSO treatment 48hpi not infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 48hpi
DMSO_48_U_3

value: Phtheirospermum Okayama anr Arabidopsis Col-23

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Arabidopsis at 48hpi


title: Day7 H3K27me3 Nontarget Knockdown, replicate 1, ChIP-seq

description: ChIP-seq Libraries


title: SpocH1_ES_d0

description:
SpocH1_ES_d0
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt


title: Day7 H3K27me3 Malat1 Knockdown, replicate 2, ChIP-seq

description: ChIP-seq Libraries


title: S010 [204339110049_R03C01]

value: male

value: Mesothelioma, epitheloid


title: Day7 H3K4me3 Malat1 Knockdown, replicate 2, ChIP-seq

description: ChIP-seq Libraries

value: CD8 T cells

value: Spleen


title: DMSO treatment 48hpi not infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 48hpi
DMSO_48_U_2

value: Phtheirospermum Okayama anr Arabidopsis Col-22

value: DMSO control


title: S009 [204339110029_R06C01]


title: S008 [204237150083_R07C01]

value: female

value: Lung squamous cell carcinoma, pleural carcinosis


title: SpocD9_NPC_d6

description:
SpocD9_NPC_d6
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC to NPC

value: Female

value: 6 days


title: Day7 H3K27me3 Malat1 Knockdown, replicate 1, ChIP-seq

description: ChIP-seq Libraries

value: 6-8 weeks old


title: DMSO treatment 48hpi not infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 48hpi
DMSO_48_U_1

value: Phtheirospermum Okayama anr Arabidopsis Col-21


title: SpocD9_NPC_d3

description:
SpocD9_NPC_d3
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); mutation of Spen SPOC domain

value: 3 days


title: DMSO treatment 48hpi infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 48hpi
DMSO_48_I_3

value: Phtheirospermum Okayama anr Arabidopsis Col-20

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Arabidopsis at 48hpi


title: D4.5 WT CD8, replicate 2, GRID-seq

description: GRID-seq Libraries

data_processing:
Reads were trimmed with cutadapt -l 86 --max-n 5 -o (v1.18), mapped to RNA-Linker-DNA (GTTGGATTCNNNGACACAGCTCACTCCCACACACCGAACTCCAAC) with bwa mem -k 5 -L 4 -B 2 -O 4 (v0.7.15) and sorted with samtools sort (v1.7). RNA and DNA reads were separated with GridTools matefq (https://github.com/biz007/gridtools). Reads were then mapped to the mm10 genome with bwa mem -k 17 -w 1 -T 1. GridTools evaluate was then used to correct against background and RNA-DNA mate read pair quality and quantity with bin size of 1 kb and moving windows of 10. GridTools.py evaluate function uses a gene annotation GTF (Gene transfer format) file to ensure that RNA end of the read always uniquely maps to its correct chromosomal location. Thus, during the analysis, only RNA reads that map back to its own locus will be retained. Moreover, the DNA end of the read will also be unique mapped, ensuring that both the RNA and DNA ends of each read are all unique reads. No read that maps to multiple locations in the genome (including repeat elements all over chromosomes) will be retained during analysis. GridTools RNA was used to identify expression levels of chromatin-enriched RNA. GridTools matrix was used to construct an interaction contact matrix of chromatin-associated RNA within specified genomic bin sizes of 1 kb or 100 kb. All lncRNAs with reads per kilobase DNA read density ³10 on any genomic region were filtered from the interaction contact matrix. A 1 kb interaction matrix was directly visualized on a heatmap using the ComplexHeatmap package (v2.2.0). PCA, k-means clustering set to 3 clusters, and pearson correlation analysis were performed on the interaction matrix with the R stats package (v3.6.2) removing all bins with zero interactions. The correlation matrix was visualized with corrplot package (v0.89) and circos plots with the circlize package (v0.42). Differential RNA chromatin interaction regions were determined by taking the average RNA interaction level of each genomic bin for all lncRNAs in a cluster. These averaged genomic bins were annotated to the transcription start site of the nearest gene using the ChIPpeakAnno. Consecutive genomic bins annotated to a single gene with greater RNA interaction for each genomic bin in one cluster relative to another cluster were considered differentially interacting. Differential RNA chromatin interaction regions were annotated with ChiPseeker.
none provided by the submitter
Assembly: mm10
Supplementary files format and content: Expression and scope Cis and Trans of all chromatin enriched RNAs

extract_protocol:
Spleens from P14 mice were homogenized, and 1x106 cells/mL in TCM were pulsed with 1 ng/ml LCMV GP33–41 peptide for 1 hour at 37°C. Cells were washed once with equal volume of warm TCM, then plated in a 96 well-plate at 5x104 cells/well. Cells were harvested 4.5 days later and dead cells removed using the Dead Cell Removal kit according to the manufacturer’s protocol (Miltenyi Biotec, Catalog number: 130-010-101). CD8+ T cells were then enriched using the CD8a+ T Cell Isolation Kit.
Cells were then cross-linked, nuclei isolated and GRID-seq libraries prepared as described previously (Li et al., 2017; Zhou et al., 2019).
GRID-seq

value: CD8 T cells


title: S007 [204234650162_R01C01]

value: male

value: Pleomorphic lung carcinoma, lung squamous cell carcinoma with >10% spindle cells


title: Day7 H3K4me3 Malat1 Knockdown, replicate 1, ChIP-seq

description: ChIP-seq Libraries

value: Spleen


title: D4.5 WT CD8, replicate 1, GRID-seq

description: GRID-seq Libraries


title: DMSO treatment 48hpi infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 48hpi
DMSO_48_I_2

value: Phtheirospermum Okayama anr Arabidopsis Col-19

value: DMSO control


title: SpocD9_ES_d1

description:
SpocD9_ES_d1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC

value: 1 day


title: SpocD9_ES_d0

description:
SpocD9_ES_d0
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: Female


title: S005 [204088030039_R06C01]

value: female

value: Lung squamous cell carcinoma, pleural carcinosis


title: SpocC11_ES_d1

description:
SpocC11_ES_d1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast


title: DMSO treatment 24hpi not infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
DMSO_24_U_3

value: Phtheirospermum Okayama anr Arabidopsis Col-17

value: Arabidopsis at 24hpi


title: S004 [204088030039_R05C01]


title: Day7 Nontarget, replicate 2, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads from scRNA-seq were aligned to mm10 using the 10x Genomics Cell Ranger software (v 2.1.0). Reads were collapsed into unique molecular identifier counts. All samples had >2000 cells detected with >1000 genes per cells with >70% of the coding genome covered.  Genes that were not expressed in at least 5% of all cells were excluded. As previously described (Boland et al., 2020), replicates of single cell libraries were normalized removing batch effects using RUVnormalize (v1.15.0). The raw UMI matrix was scaled and input to the naiveRandRUV function with parameters coeff=1e-3 and k=10. Fifty negative control genes were taken from a list of housekeeping genes (Eisenberg and Levanon, 2013) with least variability in all datasets. Seurat (v3.0.1) functions were used to calculate top variable genes, principal components analysis (PCA), and tSNE with FindVariableGenes, RunPCA, and RunTSNE. The top 5000 genes were considered as input for the PCA calculation, and only the top 25 principal components (PCs) were used in tSNE.
none provided by the submitter
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Malat1 Knockdown and Nontarget P14 CD8+ T cells were sorted 7 days after LCMV infection and resuspended in phosphate-buffered saline (PBS) + 0.04% (w/v) bovine serum albumin
10,000 cells per sample were loaded into Single Cell A chips and partitioned into Gel Bead In-Emulsions in a Chromium Controller (10x Genomics). Single-cell RNA (scRNAseq) libraries were prepared with 10x Genomics Chromium Single Cell 3′ Reagent Kits v2 according to the manufacturer’s protocol

value: 6-8 weeks old


title: Day7 Nontarget, replicate 1, scRNAseq

description: 10x Genomics


title: SpocC11_ES_d0

description:
SpocC11_ES_d0
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); mutation of Spen SPOC domain


title: Day7 Malat1 Knockdown, replicate 2, scRNAseq

description: 10x Genomics


title: DMSO treatment 24hpi not infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
DMSO_24_U_2

value: Phtheirospermum Okayama anr Arabidopsis Col-16

value: root tissue including the haustorium formation site and 1-2 mm above and below it


title: DelPID_SPOC_G3_NPC_d6

description:
DelPID_SPOC_G3_NPC_d6
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); Deletion of Xist B/C repeat (PID region)

value: 6 days


title: Day7 Malat1 Knockdown, replicate 1, scRNAseq

description: 10x Genomics

value: CD8 T cells

value: Spleen


title: S002 [204068280039_R08C01]

value: Pleomorphic lung carcinoma, lung adenocarcinoma with >10% spindle cells


title: S003 [204088030039_R04C01]

value: male

value: Pleomorphic lung carcinoma, lung squamous cell carcinoma with >10% spindle cells


title: DMSO treatment 24hpi not infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
DMSO_24_U_1

value: Phtheirospermum Okayama anr Arabidopsis Col-15

value: DMSO control


title: DelPID_SPOC_G3_NPC_d3

description:
DelPID_SPOC_G3_NPC_d3
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: Female

value: 3 days


title: S001 [203821710032_R07C01]


title: DelPID_SPOC_G3_ES_d1

description:
DelPID_SPOC_G3_ES_d1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC

value: 1 day


title: DMSO treatment 24hpi infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
DMSO_24_I_3

value: Phtheirospermum Okayama anr Arabidopsis Col-14

value: Arabidopsis at 24hpi


title: S006 [204088030039_R07C01]

value: Lung squamous cell carcinoma, pleural carcinosis


title: DMSO treatment 48hpi infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 48hpi
DMSO_48_I_1

value: Phtheirospermum Okayama anr Arabidopsis Col-18

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Arabidopsis at 48hpi


title: DelPID_SPOC_G3_ES_d0

description:
DelPID_SPOC_G3_ES_d0
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); Deletion of Xist B/C repeat (PID region)


title: DMSO treatment 24hpi infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
DMSO_24_I_2

value: Phtheirospermum Okayama anr Arabidopsis Col-13


title: DelPID_SPOC_A8_NPC_d6

description:
DelPID_SPOC_A8_NPC_d6
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC to NPC

value: 6 days


title: DMSO treatment 12hpi not infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
DMSO_12_U_3

value: Phtheirospermum Okayama anr Arabidopsis Col-11

value: Arabidopsis at 12hpi


title: BCR-ABL1+ B-ALL cells with LPS treatment X5_AIDKO_LPS

city: Xi’an

first: Yanhong

last: Ji

address: No.76 Yanta West Road

country: China

institute: Xi’an Jiaotong University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

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

value: bone marrow

tag: cell line

value: BCR-ABL1+ B-ALL cells

value: B lymphocyte

value: Aid KO

value: LPS


title: BCR-ABL1+ B-ALL cells with LPS treatment  X8_AIDKO_LPS


title: DMSO treatment 12hpi not infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
DMSO_12_U_2

value: Phtheirospermum Okayama anr Arabidopsis Col-10

value: DMSO control


title: BCR-ABL1+ B-ALL cells with LPS treatment  X2_AIDKO_LPS


title: BCR-ABL1+ B-ALL cells with LPS treatment X100_LPS_BM

value: Aid WT


title: BCR-ABL1+ B-ALL cells with LPS treatment X40_LPS_BM


title: DelPID_SPOC_A8_NPC_d3

description:
DelPID_SPOC_A8_NPC_d3
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: Female

value: 3 days


title: BCR-ABL1+ B-ALL cells with LPS treatment X6_LPS_BM


title: BCR-ABL1+ B-ALL cells with PBS treatment X7_PBS_BM

value: PBS


title: DMSO treatment 24hpi infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 24hpi
DMSO_24_I_1

value: Phtheirospermum Okayama anr Arabidopsis Col-12

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: Arabidopsis at 24hpi


title: DMSO treatment 12hpi infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
DMSO_12_I_3

value: Phtheirospermum Okayama anr Arabidopsis Col-8


title: BCR-ABL1+ B-ALL cells with PBS treatment  X1_PBS_BM


title: hfq control rep 1

city: Tempe

first: Jennifer

last: Barrila

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Center for Fundamental and Applied Microbiomics

institute: Arizona State University

description:
hfq mutant bacteria were cultured in LB for 24 hr at 37 C and 25 r.p.m. in the RWV bioreactor positioned in the control orientation.
fpkm_TPM_salonly.txt
hfq1_1xg_R1.fastq.gz.merged.fastq.gz

data_processing:
bcl2fastq v2.17.1.14 used for basecalling
STAR v2.5.1b used for alignment
Stringtie-1.3.4c was used to report FPKM values (Fragments Per Kilobase of transcript per Million mapped reads), read counts and TPM (Transcripts Per Million).
Differential expression (DE) analysis was performed with EdgeR package from Bioconductor v3.2 in R 3.2.3.
Genome_build: Human: GRCh38.p7 primary assembly; Bacteria: S. Typhimurium LT2 genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values

organism: Salmonella enterica subsp. enterica serovar Typhimurium

growth_protocol: For RNA-Seq analysis of the bacteria just prior to infection, bacteria were cultured in Lennox Broth (LB) for 24 hr at 37 C and 25 rotations per minute (r.p.m.) in RWV bioreactors positioned in the LFS and control orientations. For infection studies, the 3-D co-culture model (HT-29 and U937 cells) was grown in the RWV bioreactor for 13-14 days in GTSF-2 medium at 10% CO2.

extract_protocol:
For RNA-Seq analysis of bacteria alone just prior to infection, wild type and hfq mutant S. Typhimurium were cultured to stationary phase in RWV bioreactors, fixed in RNAlater at a 2:1 ratio (fixative: sample) and stored at -80 C until processing. Bacteria were pelleted and resuspended in 200 µL RNase-free TE buffer (ThermoFisher Scientific) containing 2 mg/mL lysozyme (Sigma-Aldrich). Samples were incubated for 10 min at room temperature with intermittent vortexing to facilitate lysis. Qiazol was added to each sample (700 µL) and incubated at room temperature for 5 min with intermittent vortexing. Samples were transferred into prepared MaXtract tubes, 0.2 µL chloroform added, and shaken for 15 sec to mix. Following a 3 min incubation at room temperature, samples were centrifuged at 12,000 x g for 15 min at 4 C. The aqueous phase was then transferred to an RNase-free microfuge tube and 1.5 volumes of 100% molecular biology grade ethanol (Sigma-Aldrich) was added to each sample and inverted to mix. Samples were applied to a miRNeasy column (Qiagen) and purified with on-column DNase I treatment. Eluted samples were quantified using a Nanodrop spectrophotometer and RNA integrity confirmed using an Agilent Bioanalyzer.     For RNA-seq analysis of the host following infection, At the specified time points, infected and time-matched uninfected 3-D co-cultures were fixed in 1 mL Qiazol (Qiagen), vortexed and stored at -80 C until processing. To extract total RNA, samples were thawed, incubated for 5 min at room temperature with intermittent vortexing, and added to a prepared High Density MaXtract tube (Qiagen). To each sample, 0.2 mL chloroform (Sigma-Aldrich) was added and tubes were shaken for 15 seconds. Following a 3 min. incubation at room temperature, samples were centrifuged at 12,000 x g for 15 min. at 4 C. The aqueous phase was then transferred to an RNase-free microfuge tube and 1.5 volumes of 200-proof molecular biology grade ethanol (Sigma-Aldrich) was added and tubes were inverted to mix. Samples were applied to miRNeasy columns (Qiagen) and purified according to manufacturer’s instructions with a 20 min. on-column DNase I treatment. Eluted samples were quantified using a Nanodrop spectrophotometer and DNase-treated a second time using the TURBO DNA-free kit (ThermoFisher). RNA integrity was confirmed on an Agilent Bioanalyzer and all samples had an RNA Integrity Number (RIN) > 9.
cDNA was prepared from total RNA using the Ovation RNA-Seq System V2 via single primer isothermal amplification (NuGEN, 7102-A01) and automated on the Apollo 324 liquid handler (Wafergen). cDNA was quantified on the Nanodrop (Thermo Fisher Scientific) and then sheared to approximately 300 bp fragments using the Covaris M220 ultrasonicator. Libraries were generated using the Kapa Biosystem library preparation kit (KK8201). Fragments were end-repaired and A-tailed as described in the Kapa protocol. Individual indexes and adapters (Bioo, 520999) were ligated onto each separate sample. Adapter-ligated molecules were cleaned using AMPure beads (Agencourt Bioscience/Beckman Coulter, A63883) and amplified with Kapa HIFI enzyme (KK2502). Each library was then analyzed for fragment size on an Agilent Tapestation and quantified by qPCR (KAPA Library Quantification Kit, KK4835) on Quantstudio 5 (ThermoFisher Scientific) before multiplex pooling and sequencing on a 1x75 flow cell on the NextSeq platform (Illumina) at the Arizona State University Genomics Core facility.

treatment_protocol: For infection studies, 3-D models were counted and evenly seeded into multiwell plates at 1x10^6 cells/well. Cells were infected at a multiplicity of infection (m.o.i.) of ~15-30 for 30 minutes, 3 hours or 24 hours with either WT or hfq mutant S. Typhimurium grown in the RWV. To eliminate extracellular bacteria, gentamicin was added to the samples at concentrations of 50 µg/mL and 10 µg/mL at the 30 minute and 3 hour time points, respectively.

value: Bacterial cell

value: chi_3339 (mouse-passaged derivative of SL1344)

tag: bacterial genotype

tag: bacterial growth orientation

value: control

tag: time post-infection


title: hfq LFS rep 2

description:
hfq mutant bacteria were cultured in LB for 24 hr at 37 C and 25 r.p.m. in the RWV bioreactor positioned in the LFS orientation.
fpkm_TPM_salonly.txt
hfq3_LS_2_R1.fastq.gz.merged.fastq.gz

value: LFS


title: DelPID_NPC_d6_Rep2

description:
DelPID_NPC_d6_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); Deletion of Xist B/C repeat (PID region)

value: 6 days


title: DelPID_SPOC_A8_ES_d1

description:
DelPID_SPOC_A8_ES_d1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC

value: 1 day


title: DMSO treatment 12hpi infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
DMSO_12_I_1

value: Phtheirospermum Okayama anr Arabidopsis Col-6

value: DMSO control

value: Arabidopsis at 12hpi


title: hfq LFS rep 3

description:
hfq mutant bacteria were cultured in LB for 24 hr at 37 C and 25 r.p.m. in the RWV bioreactor positioned in the LFS orientation.
fpkm_TPM_salonly.txt
hfq4_LS_2_R1.fastq.gz.merged.fastq.gz


title: hfq LFS rep 1

description:
hfq mutant bacteria were cultured in LB for 24 hr at 37 C and 25 r.p.m. in the RWV bioreactor positioned in the LFS orientation.
fpkm_TPM_salonly.txt
hfq1_LS_2_R1.fastq.gz.merged.fastq.gz


title: hfq control rep 2

description:
hfq mutant bacteria were cultured in LB for 24 hr at 37 C and 25 r.p.m. in the RWV bioreactor positioned in the control orientation.
fpkm_TPM_salonly.txt
hfq3_1xg_2_R1.fastq.gz.merged.fastq.gz


title: DMSO treatment 12hpi infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
DMSO_12_I_2

value: Phtheirospermum Okayama anr Arabidopsis Col-7


title: DMSO treatment 0hpi not infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
DMSO_0_U_3

value: Phtheirospermum Okayama anr Arabidopsis Col-5

value: Arabidopsis at 0hpi


title: DelPID_NPC_d3_Rep2

description:
DelPID_NPC_d3_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: Female

value: 3 days


title: DelPID_SPOC_A8_ES_d0

description:
DelPID_SPOC_A8_ES_d0
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt


title: hfq control rep 3

description:
hfq mutant bacteria were cultured in LB for 24 hr at 37 C and 25 r.p.m. in the RWV bioreactor positioned in the control orientation.
fpkm_TPM_salonly.txt
hfq4_1xg_2_R1.fastq.gz.merged.fastq.gz

value: Bacterial cell

value: chi_3339 (mouse-passaged derivative of SL1344)


title: WT control rep 2

description:
Wild type bacteria were cultured in LB for 24 hr at 37 C and 25 r.p.m. in the RWV bioreactor positioned in the control orientation.
fpkm_TPM_salonly.txt
WT3_1xg_R1.fastq.gz.merged.fastq.gz

value: wild type

value: control


title: DMSO treatment 12hpi not infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 12hpi
DMSO_12_U_1

value: Phtheirospermum Okayama anr Arabidopsis Col-9

value: root tissue including the haustorium formation site and 1-2 mm above and below it


title: wt_E12.5_DFL_HOXD13_rep2

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

description: wild type E12.5 Distal Forelimb CUT&RUN HOXD13 rep2

data_processing:
Library strategy: CUT&RUN
All command lines are available at https://github.com/lldelisle/scriptsForBoltEtAl2022
Adapter sequences and bad quality bases were removed with Cutadapt[Martin et al. 2016] version 1.16 with options -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 30 -m 15.
Reads were mapped with bowtie[Langmead et al. 2012] 2.4.1 with parameters -I 0 -X 1000 --fr --dovetail --very-sensitive on mm10 or on the II1TDOM-542 mutant genome.
Alignments with a mapping quality below 30 and discordant pairs were discarded with samtools view version 1.8 [Li et al. 2009 and Li et al. 2011].
PCR duplicates were removed with Picard[http://broadinstitute.github.io/picard/index.html] version 2.18.2 before the BAM to BED conversion with bedtools[Quinlan et al. 2010] version 2.29.2
Coverage and peak calling were computed by macs2 [Zhang et al. 2008] version 2.1.1.20160309 with options --format BED --gsize 1870000000 --call-summits --keep-dup all --bdg --nomodel --extsize 200 --shift -100.
Genome_build: mm10 or the II1TDOM-542 mutant genome
Supplementary_files_format_and_content: bigwig: coverage from macs2
Supplementary_files_format_and_content: narrowPeak: peaks from macs2

source_name: distal forelimb

growth_protocol: Crosses were made between heterozygous adults. Animals were checked for vaginal plugs on the next morning, establishing the timepoint 0.5 embryonic days. Embryos were collected 12 days later.

extract_protocol:
The distal forelimbs of embryos were dissected and placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min. Cells were then washed three times in Wash Buffer with centrifugation steps in between at 300xg for 5 minutes each.
After the CUT&RUN protocol, libraries were assembled with KAPA Hyper-Prep (07962347001)

treatment_protocol: No treatment

value: distal forelimb


title: WT control rep 3

description:
Wild type bacteria were cultured in LB for 24 hr at 37 C and 25 r.p.m. in the RWV bioreactor positioned in the control orientation.
fpkm_TPM_salonly.txt
WT4_1xg_R1.fastq.gz.merged.fastq.gz


title: DMSO treatment 0hpi not infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
DMSO_0_U_2

value: Phtheirospermum Okayama anr Arabidopsis Col-4


title: DelPID_NPC_d3_Rep1

description:
DelPID_NPC_d3_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); Deletion of Xist B/C repeat (PID region)


title: FKBP12-PCGF35_SPOC_F6_dTAG_NPC_d6

description:
d35_SPOC_F6_dTAG_NPC_d6
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); Degron FKBP12-PCGF3/5; mutation of Spen SPOC domain

value: 6 days

value: 100uM dTAG-13 12hrs before Dox


title: DelPID_NPC_d6_Rep1

description:
DelPID_NPC_d6_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt


title: 542_E12.5_PFL_CHIC

description: II1TDOM 542 E12.5 Proximal Forelimb Capture Hi-C

data_processing:
All command lines are available at https://github.com/lldelisle/scriptsForBoltEtAl2022
Adapter sequences and bad quality bases were removed with Cutadapt[Martin et al. 2016] version 1.16 with options -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 30 -m 15.
HiCUP [Lieberman-Aiden et al. 2009] version 0.6.1 was used with bowtie2 [Langmead et al. 2012] version 2.2.6 using --re1 '^GATC'  for the digestion and the II1TDOM-542 mutant genome.
BAM was converted to juicebox format with python and bash scripts available at   https://testtoolshed.g2.bx.psu.edu/repository/download?repository_id=be5040251cd4afb7&changeset_revision=44365a4feb3b&file_type=gz
Pairs with MAPQ above 30 and where both mates map on chr2 between 72402000 and 77000000 were kept
Pairs were sorted with cooler [https://github.com/open2c/cooler] version 0.7.4 and loaded into a 5kb-binned matrix.
Matrices were then balanced with cooler with parameters: --mad-max 5 --min-nnz 10 --min-count 0 --ignore-diags 2 --tol 1e-05 --max-iters 200 --cis-only
Genome_build: II1TDOM-542 mutant genome
Supplementary_files_format_and_content: validpairs are 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: cool is the balanced matrix at 5kb-bins only in the captured region

source_name: proximal forelimb

extract_protocol:
The forelimbs of embryos were dissected into proximal and distal domains, then placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min. Cells were centrifuged at 300xg for 5 minutes and the supernatant was removed. Cells were then resuspended in ice-cold 1xPBS with PIC and centrifuged again. The cells were then fixed in 1% PFA at room temperuatre for 10 minutes. A final wash was performed and cells were frozen at -80ºC until processing for Hi-C.
Hi-C libraries were processed with the SureSelect XT library preparation kit

value: proximal forelimb

value: II1TDOM 542 (mutant)


title: wt_E12.5_DFL_HOXD13_rep3

description: reanalysis of GSM5034646


title: U87-TMZr#10

type: RNA

city: Tainan

first: Kwang-Yu

address: 367 Sheng-Li Road

country: Taiwan

institute: National Institute of Cancer Research, National Health Research Institutes

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using individual internal controls and the numbers of mitochondria-related genes were identified as being differentially expressed, by at least 1.5-fold and p-value < 0.05, between the parental and TMZ-resistance cells. The final data show the log2(fold change) values of selected genes.

label: biotin

source_name: glioblastoma

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy kit. Quality control was performed with Agilent Bioanalyser.

value: TMZ-resistance


title: wt_E12.5_DFL_HOXD13_rep1

description: wild type E12.5 Distal Forelimb CUT&RUN HOXD13 rep1


title: WT control rep 1

description:
Wild type bacteria were cultured in LB for 24 hr at 37 C and 25 r.p.m. in the RWV bioreactor positioned in the control orientation.
fpkm_TPM_salonly.txt
WT2_1xg_R1.fastq.gz.merged.fastq.gz


title: FKBP12-PCGF35_SPOC_F6_dTAG_NPC_d3

description:
d35_SPOC_F6_dTAG_NPC_d3
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: Female

value: 3 days


title: DMSO treatment 0hpi infecting rep3

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
DMSO_0_I_3

value: Phtheirospermum Okayama anr Arabidopsis Col-2

value: DMSO control

value: Arabidopsis at 0hpi


title: FKBP12-PCGF35_SPOC_F6_dTAG_ES_d0

description:
d35_SPOC_F6_dTAG_ES_d0
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC


title: wt_E12.5_DFL_HOXA13_rep3

description: wild type E12.5 Distal Forelimb CUT&RUN HOXA13 rep3

value: distal forelimb

value: wild type


title: 542_E12.5_DFL_CHIC

description: II1TDOM 542 E12.5 Distal Forelimb Capture Hi-C


title: FKBP12-PCGF35_SPOC_F6_dTAG_ES_d1

description:
d35_SPOC_F6_dTAG_ES_d1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 1 day


title: WT LFS rep 3

description:
Wild type bacteria were cultured in LB for 24 hr at 37 C and 25 r.p.m. in the RWV bioreactor positioned in the LFS orientation.
fpkm_TPM_salonly.txt
WT4_LS_R1.fastq.gz.merged.fastq.gz

value: Bacterial cell

value: chi_3339 (mouse-passaged derivative of SL1344)

value: LFS


title: DMSO treatment 0hpi infecting rep2

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
DMSO_0_I_2

value: Phtheirospermum Okayama anr Arabidopsis Col-1

value: root tissue including the haustorium formation site and 1-2 mm above and below it


title: wt_E12.5_DFL_HOXA13_rep2

description: wild type E12.5 Distal Forelimb CUT&RUN HOXA13 rep2


title: U87-MG

value: parental


title: wt_E12.5_DFL_HOXA13_rep1

description: wild type E12.5 Distal Forelimb CUT&RUN HOXA13 rep1


title: WT LFS rep 1

description:
Wild type bacteria were cultured in Lennox Broth (LB) for 24 hr at 37 C and 25 rotations per minute (r.p.m.) in the RWV bioreactor positioned in the LFS orientation.
fpkm_TPM_salonly.txt
WT2_LS_S9_R1.fastq.gz


title: FKBP12-PCGF35_SPOC_F6_ctrl_NPC_d6

description:
d35_SPOC_F6_ctrl_NPC_d6
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); Degron FKBP12-PCGF3/5; mutation of Spen SPOC domain

value: 6 days

value: untreated


title: FKBP12-PCGF35_SPOC_F6_ctrl_NPC_d3

description:
d35_SPOC_F6_ctrl_NPC_d3
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: Female

value: 3 days


title: des6fad5_wound_3

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

data_processing:
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with HISAT2
Summarization of reads was performed with HTSeq-count program
Normalization and differential expression analysis with EdgeR
Genome_build: MpTak1_v5.1
Supplementary_files_format_and_content: Text format with two columns: gene_ID and raw reads per gene

organism: Marchantia polymorpha

source_name: Leaflets

growth_protocol: Marchantia polymorpha accession Takaragaike-1 (Tak-1; male), mutant Mpcoi1 and double mutant Mpdes6fad5 were used in this work. Plants were subcultivated on 0.5 Gamborg’s B5 medium containing 1% agar for 3 weeks. Apical fragments of the plants, excluding gemma cups, were ground in liquid nitrogen prior RNA extraction. Every independent biological replicate contained 6-8 plants.

extract_protocol:
Total RNA from Marchantia was extracted with Favorgen Plant RNA Extraction and DNase on-column digestion (Qiagen) was performed to remove genomic DNA contamination.
The RNA-seq library was prepared by Novogene, using standard Illumina protocols.

treatment_protocol: Leaflets were wounded with tweezers and frozen 90 min after treatment

value: Wound, 2 hours


title: DMSO treatment 0hpi not infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
DMSO_0_U_1

value: Phtheirospermum Okayama anr Arabidopsis Col-3

value: DMSO control

value: Arabidopsis at 0hpi


title: FKBP12-PCGF35_SPOC_F6_ctrl_ES_d0

description:
d35_SPOC_F6_ctrl_ES_d0
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC


title: FKBP12-PCGF35_SPOC_F6_ctrl_ES_d1

description:
d35_SPOC_F6_ctrl_ES_d1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 1 day


title: calorie_dilution_6

city: Beijing

middle: Roger

last: Speakman

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Sub-pixel Registration used for basecalling
FASTQ raw data files were measured by using fastQC (www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) quality control tool
Raw reads were aligned to the Mus musculus reference genome (GRCm38) using HISAT2-2.1.0 (Kim et al., 2015; Pertea et al., 2016) and prebuild indexes were used (GRCm38 release 81 version of M. Musculus)
read were quantified using featureCounts (v1.5.1) (Liao et al., 2014)
Differential gene expression was modelled using the edgeR package in R (Robinson et al., 2010)
Supplementary files format and content: Excel file with gene counts for every gene and every sample

source_name: Hypothalamus

extract_protocol:
Hypothalamus was cut from total brain and total RNA was extratced using Rneasy lipid Tissue Mini Kit
RNA libraries were prepared for sequencing using standard Beijing Genomic Institute (BGI) protocols.

value: Hypothalamus

value: calorie dilution


title: 542_E11.5_DFL_HOXD13

description: II1TDOM 542 E11.5 Distal Forelimb CUT&RUN HOXD13

value: distal forelimb

value: II1TDOM 542 (mutant)


title: des6fad5_wound_2


title: 542_E12.5_DFL_HOXA13_rep1

description: II1TDOM 542 E12.5 Distal Forelimb CUT&RUN HOXA13 rep1


title: calorie_dilution_4


title: calorie_dilution_5


title: des6fad5_wound_1


title: WT LFS rep 2

description:
Wild type bacteria were cultured in LB for 24 hr at 37 C and 25 r.p.m. in the RWV bioreactor positioned in the LFS orientation.
fpkm_TPM_salonly.txt
WT3_LS_R1.fastq.gz.merged.fastq.gz

value: Bacterial cell

value: chi_3339 (mouse-passaged derivative of SL1344)

value: wild type

value: LFS


title: calorie_dilution_3


title: FKBP12-PCGF35_SPOC_F10_dTAG_NPC_d6

description:
d35_SPOC_F10_dTAG_NPC_d6
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); Degron FKBP12-PCGF3/5; mutation of Spen SPOC domain

value: 6 days

value: 100uM dTAG-13 12hrs before Dox


title: des6fad5_mock_3

value: mock, 2 hours


title: wt_E12.5_PFL_ATAC_rep2

description: wildtype E12.5 Proximal Forelimb ATAC replicate 2

data_processing:
All command lines are available at https://github.com/lldelisle/scriptsForBoltEtAl2022
Adapter sequences and bad quality bases were removed with Cutadapt[Martin et al. 2016] version 1.16 with options -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15.
Reads were mapped with bowtie[Langmead et al. 2012] 2.4.1 with parameters -I 0 -X 1000 --fr --dovetail --very-sensitive on mm10 or on the II1TDOM-542 mutant genome.
Alignments with a mapping quality below 30, discordant pairs, and reads mapping to the mitochondria, were discarded with bamtools version 2.4.0 [https://github.com/pezmaster31/bamtools].
PCR duplicates were removed with Picard[http://broadinstitute.github.io/picard/index.html] version 2.18.2 before the BAM to BED conversion with bedtools[Quinlan et al. 2010] version 2.30.0.
Coverage and peak calling were computed by macs2 [Zhang et al. 2008] version 2.1.1.20160309 with options --format BED --gsize 1870000000 --call-summits --keep-dup all --bdg --nomodel --extsize 200 --shift -100.
Genome_build: mm10 or the II1TDOM-542 mutant genome
Supplementary_files_format_and_content: bigwig: coverage from macs2
Supplementary_files_format_and_content: narrowPeak: peaks from macs2

extract_protocol:
The forelimbs or forebrains of embryos were dissected and placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min. Cells were counted and 50,000 cells were isolated for processing with the Nextera Tn5 enzyme (Illumina FC-131-1096) as previously described (Buenrostro NatMeth 2013).
Tn5 treated DNA was amplified with Nextera Library primers using NEBNext library amplification master mix (NEB M0541).

value: proximal forelimb


title: calorie_dilution_2


title: des6fad5_mock_2


title: wt_E12.5_PFL_ATAC_rep1

description: wildtype E12.5 Proximal Forelimb ATAC replicate 1


title: des6fad5_mock_1


title: calorie_dilution_1


title: FKBP12-PCGF35_SPOC_F10_dTAG_NPC_d3

description:
d35_SPOC_F10_dTAG_NPC_d3
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: Female

value: 3 days


title: wt_E12.5_FB_ATAC_rep2

description: wildtype E12.5 Forebrain ATAC replicate 2

source_name: forebrain

value: forebrain


title: DMSO treatment 0hpi infecting rep1

description:
2mm or root tip Phtheirospermum and Arabidopsis at 0hpi
DMSO_0_I_1

value: Phtheirospermum Okayama anr Arabidopsis Col-0

value: root tissue including the haustorium formation site and 1-2 mm above and below it

value: DMSO control

value: Arabidopsis at 0hpi


title: 542_E12.5_DFL_HOXA13_rep2

description: II1TDOM 542 E12.5 Distal Forelimb CUT&RUN HOXA13 rep2

value: distal forelimb

value: II1TDOM 542 (mutant)


title: calorie_restriction_6

value: Hypothalamus

value: calorie restriction


title: FKBP12-PCGF35_SPOC_F10_dTAG_ES_d0

description:
d35_SPOC_F10_dTAG_ES_d0
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: mESC


title: wt_E12.5_FB_ATAC_rep1

description: wildtype E12.5 Forebrain ATAC replicate 1

value: wild type


title: calorie_restriction_4


title: calorie_restriction_3


title: mpcoi1_wound_3

value: Wound, 2 hours


title: wt_E12.5_DFL_ATAC_rep2

description: wildtype E12.5 Distal Forelimb ATAC replicate 2


title: FKBP12-PCGF35_SPOC_F10_ctrl_NPC_d3

description:
d35_SPOC_F10_ctrl_NPC_d3
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC to NPC

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); Degron FKBP12-PCGF3/5; mutation of Spen SPOC domain

value: untreated


title: calorie_restriction_2


title: FKBP12-PCGF35_SPOC_F10_ctrl_ES_d1

description:
d35_SPOC_F10_ctrl_ES_d1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: Female

value: 1 day


title: wt_E12.5_DFL_ATAC_rep1

description: wildtype E12.5 Distal Forelimb ATAC replicate 1


title: FKBP12-PCGF35_SPOC_F10_ctrl_ES_d0

description:
d35_SPOC_F10_ctrl_ES_d0
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt


title: FKBP12-PCGF35_SPOC_F10_ctrl_NPC_d6

description:
d35_SPOC_F10_ctrl_NPC_d6
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 6 days


title: calorie_restriction_1


title: 542_E12.5_PFL_ATAC_rep2

description: II1TDOM 542 E12.5 Proximal Forelimb ATAC replicate 2

value: proximal forelimb


title: FKBP12-PCGF35_SPOC_F10_dTAG_ES_d1

description:
d35_SPOC_F10_dTAG_ES_d1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 100uM dTAG-13 12hrs before Dox


title: 542_E12.5_PFL_ATAC_rep1

description: II1TDOM 542 E12.5 Proximal Forelimb ATAC replicate 1


title: FKBP12-PCGF35_dTAG_NPC_d6_Rep2

description:
d35_dTAG_NPC_d6_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); Degron FKBP12-PCGF3/5


title: control_hypo_6

value: control


title: mpcoi1_mock_2

value: mock, 2 hours


title: mpcoi1_wound_2


title: control_hypo_5

value: Hypothalamus


title: mpcoi1_mock_1


title: tak1_wound_3


title: FKBP12-PCGF35_dTAG_NPC_d6_Rep1

description:
d35_dTAG_NPC_d6_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt


title: mpcoi1_mock_3


title: 542_E12.5_FB_ATAC_rep1

description: II1TDOM 542 E12.5 Forebrain ATAC replicate 1

value: forebrain

value: II1TDOM 542 (mutant)


title: FKBP12-PCGF35_dTAG_NPC_d3_Rep2

description:
d35_dTAG_NPC_d3_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: 3 days


title: control_hypo_4


title: mpcoi1_wound_1

value: Wound, 2 hours


title: tak1_wound_2


title: control_hypo_3


title: tak1_wound_1


title: 542_E12.5_DFL_ATAC_rep1

description: II1TDOM 542 E12.5 Distal Forelimb ATAC replicate 1

value: distal forelimb


title: 542_E12.5_DFL_ATAC_rep2

description: II1TDOM 542 E12.5 Distal Forelimb ATAC replicate 2


title: control_hypo_2


title: FKBP12-PCGF35_dTAG_NPC_d3_Rep1

description:
d35_dTAG_NPC_d3_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC to NPC


title: tak1_mock_3


title: control_hypo_1


title: tak1_mock_1


title: Silk_4 wks

city: Seoul

first: YOON-SEOB

last: KIM

state: Korea (the Republic of)

address: Banpodaero 222

country: South Korea

institute: The Catholic University of Korea

data_processing:
Libraries were sequenced on HiSeq X instruments
Using CellRanger 3.0.0 pipeline (10X Genomics), fastq data was aligned to a mouseh genome reference (mm10) and the unique molecular identifier (UMI) counts was quantified .
The raw gene expression matrix from the CellRanger pipeline was filtered using the Seurat R package (version 3.0) and selected according to the following criteria: cells with > 200 genes, and < 8,000 genes, and < 25% of mitochondrial gene expression in UMI counts.
After filtering step, the raw gene expression matrix was normalized to the total UMI counts per cell and transformed to the natural log scale.
Further clustering and analysis were done under Seurat pipeline
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content: Tab-deliminated text file containing the raw gene expression (raw_counts.txt.gz) for QC filtered cells, and cell annotation file (meta_data.txt.gz).

source_name: Foriegn body granuloma, Silk_4 wks

extract_protocol:
The cells were washed in PBS (0.04% BSA) and resuspended at a concentration of ~1000 cells/μl.
The cells were used for generating scRNA-seq libraries using Chromium Single-cell 3' Reagent Kits v3 (10x Genomics, Pleasanton, CA) according to the manufacturer’s protocol.

value: Foriegn body granuloma, Silk_4 wks


title: FKBP12-PCGF35_dTAG_ES_d1_Rep1

description:
d35_dTAG_ES_d1_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC

value: Female


title: tak1_mock_2


title: Antibiotic

city: New York

first: Joshua

middle: Caleb

last: Leinwand

state: NY

address: 177 Fort Washington Ave, 7th Floor

department: Surgery

institute: Columbia University Irving Medical Center

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: mm10
Supplementary_files_format_and_content: genes-barcodes (tsv file), matrices (matrix file)

source_name: Liver

extract_protocol:
Single cell RNA sequencing was performed using the 10X Chromium platform, following manufacturer's protocol.
Library construction was performed using the 10X Genomics platform using Chromium™ Single Cell 3' v2 Reagent Kits and a Chromium instrument according to the manufacturer’s protocol
single cell RNA-seq

treatment_protocol: Mouse drinking water was mixed with ampicillin (1 mg/mL; Santa Cruz Biotech), vancomycin (0.5 mg/mL; Sigma), neomycin (0.5 mg/mL; Sigma), and metronidazole (1 mg/mL; Santa Cruz Biotech). FACS-sorting was performed on the SY3200 (Sony, Tokyo, Japan). Cell pellets were re-suspended and cell labeling was performed after blocking Fc_RIII/II with an anti-CD16/CD32 mAb (eBioscience, San Diego, CA) by incubating 1x106 cells with 1ug of fluorescently conjugated mAbs directed against mouse CD45 (30-F11).

value: Liver

value: CD45+ inflammatory cells

value: Ampicillin, Metronidazole, Neomycin, Vancomycin


title: FKBP12-PCGF35_dTAG_ES_d0_Rep1

description:
d35_dTAG_ES_d0_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); Degron FKBP12-PCGF3/5

value: 100uM dTAG-13 12hrs before Dox


title: QBC-939 cells, Knockdown of ANXA10 1

city: jinan

first: qi

middle: rong

last: sun

state: shandong

address: wenhuxi road 107

institute: qilu hospitai

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs

source_name: human cholangiocarcinoma cell

extract_protocol:
QBC-939 cells were harvested, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cholangiocarcinoma Cell Line QBC-939

value: Knockdown of ANXA10 using sh-RNA


title: QBC-939 cells, Knockdown of ANXA10 2


title: Sponge_2 wks

source_name: Foriegn body granuloma, Sponge_2 wks

value: Foriegn body granuloma, Sponge_2 wks


title: QBC-939 cells, control 3

value: control


title: FKBP12-PCGF35_ctrl_NPC_d3_Rep2

description:
d35_ctrl_NPC_d3_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: untreated


title: QBC-939 cells, Knockdown of ANXA10 3


title: Control

value: Vehicle


title: FKBP12-PCGF35_dTAG_ES_d0_Rep2

description:
d35_dTAG_ES_d0_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt


title: Silk_2 wks

source_name: Foriegn body granuloma, Silk_2 wks

value: Foriegn body granuloma, Silk_2 wks


title: CMC_Visium_Sponge_2 wks

data_processing:
Libraries were sequenced on HiSeq X instruments
Using SpaceRanger pipeline (10X Genomics), fastq data was aligned to a mouseh genome reference (mm10) and the unique molecular identifier (UMI) counts was quantified .
The raw gene expression matrix from the CellRanger pipeline was processed using the Seurat R package (version 3.0) function SCTransform.
Further clustering and analysis were done under Seurat pipeline
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content: Tab-deliminated text file containing the raw gene expression (visium_raw_counts.txt.gz) for QC filtered cells, and cell annotation file (visium_meta_data.txt.gz).

extract_protocol:
An FBR sample (sponge, 2 weeks) was frozen in optimal cutting temperature medium and stored at −80 °C until sectioning.
After adjusting tissue permeabilization time to 18 min, we performed spatial sequencing library construction using Visium Spatial Gene Expression Reagent Kits (10x Genomics), according to the manufacturer’s instructions.


title: QBC-939 cells, control 1


title: FKBP12-PCGF35_ctrl_NPC_d6_Rep2

description:
d35_ctrl_NPC_d6_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC to NPC

value: 6 days


title: FKBP12-PCGF35_ctrl_NPC_d6_Rep1

description:
d35_ctrl_NPC_d6_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt


title: QBC-939 cells, control 2


title: FKBP12-PCGF35_dTAG_ES_d1_Rep2

description:
d35_dTAG_ES_d1_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC

value: 1 day


title: Sponge_4 wks

source_name: Foriegn body granuloma, Sponge_4 wks

value: Foriegn body granuloma, Sponge_4 wks


title: Control

source_name: Thioglycollate-elicited macrophages

value: Thioglycollate-elicited macrophages


title: TSA-PD4_IgG_WT_Rep1

first: Jin Yong

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of Dermatology

institute: Seoul National University College of Medicine

data_processing:
Sequencing reads were aligned using Bowtie2 v1.1.1 with the parameters “-X2000 --very-sensitive” for paired-end reads. Duplicates were removed using Picard v2.7.1.
Peaks for each replicate were called using MACS2 v2.1.2 with the parameter “-f BEDPE -q 0.001 --nomodel --call-summits”.
ATAC peak files per each sample were merged to achieve a consensus peak file representing peaks that were called across all samples.
Deeptools v3.4.2 bamCoverage (ATAC-seq) or bamCompare (ChIP-seq) function was used to generate bigWigs of bam files for the consensus peak regions.
For quantitative analysis of ChIP-seq, H3K27ac signals of each timepoint were normalized to merged input signals with scale factors calculated by the total amount ratio of H3K27ac protein to H3 protein.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: FACS-sorted CD140a+CD26+ dermal fibroblasts after in vivo TSA treatment

extract_protocol:
Freshly FACS-sorted CD140a+CD26+ cells from mouse dermis were subjected to ATAC-seq and ChIP-seq library preparation.
For ATAC-seq, cells were incubated with cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), then were immediately subjected to a transposition reaction for 30 min at 37°C with TN5 transposase (Illumina). Transposed DNA was purified using Qiagen MiniElute purification kit and PCR amplified with 10-15 cycles. Library construction was performed using Nextera primers (Illumina). The libraries were sequenced using Illumina HiSeq 2500 platform using a 50-bp paired-end setting. ATAC-seq experiments were independently repeated for two times.  For ChIP-seq, library preparation was performed using ChIPmentation method (Nat Methods 12, 963–965 (2015).). Briefly, cells were fixed with 1% paraformaldehyde in PBS for 10 min at 25C, then were collected at 500 g for 10 min at 4°C and washed twice with 1 μM phenylmethyl sulfonyl fluoride (PMSF) in PBS. The pellet was sonicated a Branson 102C sonicator on ice until the size of fragments was in the range of 200–700 bp. The lysate was centrifuged and the supernatant containing the sonicated chromatin was transferred to a new tube. The sonicated lysate was brought to in 200 μl RIPA buffer per immunoprecipitation. For each immunoprecipitation, 10 μl Dynabeads Protein A were washed twice and resuspended with 0.1% BSA in PBS. The antibody was added and bound to the beads by rotating for 2 h at 4 °C. Anti-H3K27ac antibody (1 μg per immunoprecipitation, Diagenode pAB-196-050) and a nonspecific IgG rabbit antibody (2.5 μg per immunoprecipitation, Millipore 12-370) were used. Blocked antibody-conjugated beads were then placed on a magnet, supernatant was removed, and the sonicated lysate was added to the beads followed by incubation by rotating for 3 h at 4°C. Beads were washed subsequently with RIPA, RIPA-HS and RIPA-LiCl buffers. Beads were washed with cold Tris-HCl pH 8.0 and then resuspended in 25 μl tagmentation reaction buffer (10 mM Tris pH 8.0, 5 mM MgCl2, 10% v/v dimethylformamide) containing 1 μl TN5 transposase enzyme (Illumina) and incubated for 5 min at 37 °C in a thermocycler. Beads were washed with RIPA and cold Tris-HCl pH 8.0 and then incubated with 70 μl elution buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.4% SDS) containing 2 μl of Proteinase K (NEB) for 1 h at 55 °C and for 6 h at 65 °C, and supernatant was transferred to a new tube. Transposed DNA was purified with Qiagen MiniElute purification kit, and PCR amplified using Kapa HiFi HotStart ReadyMix (Kapa Biosystems). Enriched libraries were purified using SPRI AMPure XP beads at a beads-to-sample ratio of 1:1, followed by a size selection using AMPure XP beads to recover libraries with a fragment length of 200–400 bp. Library construction was performed using TruSeq ChIP Library Preparation Kit (Illumina). The libraries were sequenced using Illumina HiSeq 2500 platform using a 100-bp paired-end setting.

tag: developmental stage

tag: agent

value: TSA

tag: antibody

value: IgG


title: Drosophila-Kc-ph+E(z)+CtBP RNAi-2

city: Nangjing

first: Ming

last: Fang

state: jiangsu

address: 2 Sipailou Road

institute: Southeast University

data_processing:
Reads were mapped to the D. melanogaster genome (dm6, The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomics) using Bowtie 2 version 2.2.6 (Langmead and Salzberg, 2012) with default parameters.
Splice junctions were determined from the mapped reads using TopHat version 2.1.0 (Kim et al., 2013) with default values.
Cufflink (v 2.2.1) (Trapnell et al., 2012a) was used for calculating expression levels in FPKM (fragments per kilobase of exon per million fragments mapped), data visualization and measuring expression levels.
The Cuffdiff program within Cufflinks was used to test for statistically significant differences in transcript expression between different RNAi treated cells.
The downstream statistical analyses and plots were performed in R (v3.2.3; http://www.r-project.org/). Identification of differentially expressed genes was performed with R package CummeRbund v2.14.0 (Goff, 2013).
Genome_build: dm6
Supplementary_files_format_and_content: csv file include FPKM values for all 9 Samples.

organism: Drosophila melanogaster

growth_protocol: Kc cells were kept with shneiders' drosophila medium (Gibco) with 5% FBS

extract_protocol:
RNAi treated Kc cells were harvested and total RNA was extracted using Trizol reagent. Then the RNA was sent to BGI (Shenzhen, China) for their deep sequencing platform build on the Illumina HiSeqTM 2000.
RNA libraries were prepared by BGI (Shenzhen, China) for sequencing using standard Illumina protocols

treatment_protocol: Kc cells were cultured in serum-free medium and dsRNAs were added by 15 μg per two millions of cells.  After an hour incubation, 1.0 ml of media containing 7.5% FBS was added.  Cells were harvested on the seventh day for RNA extraction.

tag: RNAi

value: ph+E(z)+CtBP RNAi-2


title: Drosophila-Kc-ph+E(z)+CtBP RNAi-3

value: ph+E(z)+CtBP RNAi-3


title: FKBP12-PCGF35_ctrl_NPC_d3_Rep1

description:
d35_ctrl_NPC_d3_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

data_processing:
The standard ChrRNA-seq data mapping pipeline is reported in our previous study (Nesterova et al., 2019). Briefly, raw fastq files of read pairs were first mapped to rRNA by bowtie2 (v2.3.2; Langmead and Salzberg 2012) and rRNA-mapping reads discarded (typically <2%). The remaining unmapped reads were aligned to an N-masked mm10 genome with STAR (v2.4.2a; Dobin et al., 2013) using parameters: “-outFilterMultimapNmax 1 -outFilterMismatchNmax 4 -alignEndsType EndToEnd”.
Aligned reads were assigned to separate files for either the Cast or Dom/129S genomes by SNPsplit (v0.2.0; Krueger and Andrews, 2016) using the “- paired” parameter and a SNPfile containing the 23,005,850 SNPs between Cast and Dom/129S genomes (UCSC).
Read fragments overlapping genes, for both the ‘unsplit’ and ‘allelic’ files of each sample, were counted by the program featureCounts (Liao et al., 2014) using an annotation file of all transcripts and lncRNAs from NCBI RefSeq and the parameters “-t transcript -g gene id -s 2”.
Further allelic analysis was performed using R and RStudio on allelic count matrix output files from featureCounts. X-linked genes with at least 10 allelically-assigned fragments (i.e. containing reads that overlap SNPs) in >80% of WT samples were retained for gene silencing analysis. Gene silencing was assessed by calculating the allelic ratio of read counts, given by Xi/(Xi + Xa). An additional filter on the allelic ratio in uninduced mESCs (0.1 < allelic ratio < 0.9) was also applied, as strongly monoallelic genes are likely to be technical artifacts of singular mis-annotated SNPs.
Genome_build: mm10
Supplementary_files_format_and_content: counts tables, allelic ratio

source_name: iXist-ChrX-Dom(mESC)

extract_protocol:
Between 5 x 106 (NPC) and 3 x 107 (mESC) cells were collected from confluent 90mm dishes, washed once with PBS, then snap-frozen and stored at -80oC. Chromatin extraction was performed as follows: Cell pellets were lysed on ice for 5 min in RLB (10 mM Tris pH7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40). Nuclei were then purified by centrifugation through 24% sucrose/RLB (2800 g for 10 min at 4oC), resuspended in NUN1 (20 mM Tris pH7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.1 mM DTT), and then lysed by gradual addition of an equal volume NUN2 (20 mM HEPES pH 7.9, 300 mM NaCl, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea, 0.1 mM DTT). After 15 min incubation on ice with occasional vortexing, the chromatin fraction was isolated as the insoluble pellet after centrifugation (2800 g for 10 min at 4oC). Chromatin pellets were resuspended in 1mL TRIzol (Invitrogen) and fully homogenenized and solubilized by eventually being passed through a 23-gauge needle 10 times . This was followed by isolation of chromatin-associated RNA through TRIzol/chloroform extraction with isopropanol precipitation. Precipitated RNA pellets were washed twice with 70% ethanol. Final ChrRNA samples were then resuspended in H2O, treated with TurboDNAse and measured by Nanodrop (both ThermoFisher). 500 ng – 1 µg of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit (RS-122-2301).
Illumina TruSeq stranded total RNA kit (500 ng – 1 µg of RNA)

value: Female

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele); Degron FKBP12-PCGF3/5

value: 3 days


title: Drosophila-Kc-ph+E(z)+CtBP RNAi-1

value: ph+E(z)+CtBP RNAi-1


title: FKBP12-PCGF35_ctrl_ES_d0_Rep2

description:
d35_ctrl_ES_d0_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: 129S x Cast

value: untreated


title: FKBP12-PCGF35_ctrl_ES_d1_Rep1

description:
d35_ctrl_ES_d1_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt


title: PD2_IgG_WT_Rep1

source_name: FACS-sorted CD140a+CD26+ dermal fibroblasts


title: PD0_IgG_WT_Rep1


title: PD4_IgG_WT_Rep1


title: FKBP12-PCGF35_ctrl_ES_d0_Rep1

description:
d35_ctrl_ES_d0_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt


title: TSA-PD4_H3K27ac_WT_Rep1


title: PD4_H3K27ac_WT_Rep1


title: iXist-ChrX-Dom_NPC_JB_d6_Rep2

description:
A11B2_NPC_JB_d6_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele)


title: Drosophila-Kc-ph+E(z) RNAi-2

value: ph+E(z) RNAi-2


title: Drosophila-Kc-Control RNAi-3

value: Control RNAi-3


title: Drosophila-Kc-ph+E(z) RNAi-1

value: ph+E(z) RNAi-1


title: iXist-ChrX-Dom_NPC_JB_d3_Rep2

description:
A11B2_NPC_JB_d3_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC to NPC


title: PD2_H3K27ac_WT_Rep1


title: iXist-ChrX-Dom_NPC_JB_d3_Rep1

description:
A11B2_NPC_JB_d3_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt


title: PD0_H3K27ac_WT_Rep1


title: FKBP12-PCGF35_ctrl_ES_d1_Rep2

description:
d35_ctrl_ES_d1_Rep2
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

value: mESC

value: 1 day


title: Drosophila-Kc-Control RNAi-2

value: Control RNAi-2


title: FKBP12-PCGF35_NoDox0h_H2AK119ub1_Rep2

data_processing:
Raw fastq read pairs were mapped to the “N-masked” the N-masked mm10 genome concatenated with the dm6 Drosophila genome by bowtie2 (v2.2.6) using parameters “--very-sensitive --no-discordant --no-mixed -X 2000”
Alignment files were filtered to remove unmapped read pairs and PCR duplicates (picard-tools MarkDuplicates). Bam files were then sorted and indexed using samtools commands.
Sequencing reads mapping to mm10 and dm6 genomes were counted for each sample using "samtools view" commands. Calibration factors were then calculated according to the derived formula for occupancy ratio (ORi) (Hu et al., 2015) and are provided in Supplemental File 2 of associated publication.
Alignments files were processed into bedGraph format by genomeCoverageBed (BEDtools), normalised to the total library size of the sample, and scaled by calibration factor.
BigWig files were generated using samtools bamCoverage and scaled by library size and calibration factor.
The custom script ExtractInfoFrombedGraph_AtBed.py (https://github.com/guifengwei) was used on calibrated bedGraph files to extract values for windows 250 kb of the 103.5Mb region of ChrX1 proximal to Xist that can be allelically-assigned. Line graphs displayed in report were generated in R by further transformation of these windowed files: first enrichment over a combined input file (IP/input for each allelic file), then differential allelic enrichment (Xi - Xa) for each window.
Genome_build: mm10; dm6
Supplementary_files_format_and_content: txt (tables of calibrated ChIP signal for 250KB windows); bigwig

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged and colleced with TrypLE (ThermoFisher) and frozen in FCS + 10% DMSO. Mitomycin C-inactivated mouse fibroblasts were used as feeders and removed prior to plating out for experiments by pre-plating.

extract_protocol:
Calibrated native ChIP-seq was performed largely as described in our previous studies (Nesterova et al., 2019; Rodermund et al., 2021) using buffers supplemented with 5 mM of the deubiquitinase inhibitor N-ethylmaleimide (Merck Life Science) for H2AK119ub1 ChIP. 4 x 107 mESCs and 1 x 107 Drosophila Sg4 Cells (20% cellular spike-in) were carefully counted using a Countess 3 Automated Cell Counter (ThermoFisher) and pooled. Cells were then lysed in RSB (10 mM Tris pH8, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) for 5 min on ice with gentle inversion before nuclei collection by centrifugation (1500 g for 5 min at 4oC). Nuclei were resuspended in 1 mL of RSB + 0.25 M sucrose + 3 mM CaCl2, treated with 200U of MNase (Fermentas) for 5 min at 37oC, quenched with 4 µl of 1M EDTA, then centrifuged at 2000 g for 5 min. The supernatant was transferred to a fresh tube as fraction S1. The remaining chromatin pellet was incubated for 1 hour in 300 µl of nucleosome release buffer (10 mM Tris pH7.5, 10 mM NaCl, 0.2 mM EDTA), carefully passed five times through a 27G needle, and then centrifuged at 2000 g for 5 min. The supernatant from this S2 fraction was combined with S1 to make the final soluble chromatin extract. For each ChIP reaction, 100 µl of chromatin was diluted in Native ChIP incubation buffer (10 mM Tris pH 7.5, 70 mM NaCl, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton) to 1 mL and incubated with Ab overnight at 4 °C. Samples were incubated for 1 hour with 40 µl protein A agarose beads pre-blocked in Native ChIP incubation buffer with 1 mg/mL BSA and 1 mg/mL yeast tRNA, then washed a total of four times with Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once with TE pH 7.5. All washes were performed at 4oC. The DNA was eluted from beads by resuspension in elution buffer (1% SDS, 100 mM NaHCO3) and shaking at 1000rpm for 30 min at 25oC, and was purified using the ChIP DNA Clean and Concentrator kit (Zymo Research).
Libraries were prepared from 25-100ng ChIP DNA using NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1μg/mL) to the culture medium for 24h. For PCGF3/5 degradation, dTAG-13 was added at 100uM 12 hours prior to Xist (Dox) induction.

value: Dom/129S x Cast

value: Endogenous Xist promoter replaced with TetOn Promoter (Dom/129S allele); Degron FKBP12-PCGF3/5

tag: chip antibody

value: anti-H2AK119ub1 (CST #8240S, rabbit mAb D27C4)

tag: spike-in

value: 20% cellular spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: TSA-PD4_ATAC_WT_Rep1

value: TSA


title: Drosophila-Kc-Control RNAi-1

value: Control RNAi-1


title: PD4_ATAC_WT_Rep2


title: Drosophila-Kc-ph+E(z) RNAi-3

value: ph+E(z) RNAi-3


title: 131/4-5B2

data_processing:
Libraries were sequenced on HiSeq 2500 instruments
Using CellRanger 3.0.0 pipeline (10X Genomics), fastq data was aligned to a mouseh genome reference (mm10) and the unique molecular identifier (UMI) counts was quantified .
The raw gene expression matrix from the CellRanger pipeline was filtered using the Seurat R package (version 3.0) and selected according to the following criteria: cells with > 3000 genes, and < 7,000 genes, and < 0.2% of mitochondrial gene expression in UMI counts.
After filtering step, the raw gene expression matrix was normalized to the total UMI counts per cell and transformed to the natural log scale.
Further clustering and analysis were done under Seurat pipeline
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Tab-deliminated text file containing the raw gene expression (UMI_raw_counts.txt) and the normalized gene expression (Natural_log_UMI_matrix.txt) for QC filtered cells, and cell annotation file.

extract_protocol:
The cells were washed in PBS (0.04% BSA) and resuspended at a concentration of ~1000 cells/μl.
The cells were used for generating scRNA-seq libraries using Chromium Single-cell 3' Reagent Kits v2 (10x Genomics, Pleasanton, CA) according to the manufacturer’s protocol.

tag: phenotype

value: high potential of brain metastasis


title: WM239A

value: poorly metastatic melanoma cell line


title: FKBP12-PCGF35_NoDox0h_H2AK119ub1_Rep1

tag: Sex

value: Female


title: iXist-ChrX-Dom_NPC_JB_d6_Rep1

description:
A11B2_NPC_JB_d6_Rep1
SPOCmut_Polycomb_ChrXAllelicRatio_table.txt

tag: strain

value: 129S x Cast

value: Endogenous Xist promoter replaced with TetOn Promoter (129S allele)

value: 6 days


title: 113/6-4L

source_name: 113/6-4L (WM239A subclone)

value: high potential of lung metastasis

value: 113/6-4L (WM239A subclone)


title: FKBP12-PCGF35_dTAG36h_Dox24h_H2AK119ub1_Rep1

tag: cell type

value: mESC


title: PD0_ATAC_WT_Rep2


title: PD4_ATAC_WT_Rep1


title: FKBP12-PCGF35_Dox24h_H2AK119ub1_Rep2

tag: cell engineering


title: FKBP12-PCGF35_dTAG36h_Dox24h_H2AK119ub1_Rep2


title: PD2_ATAC_WT_Rep1


title: FKBP12-PCGF35_Dox24h_H2AK119ub1_Rep1


title: PD0_ATAC_WT_Rep1


title: FKBP12-PCGF35_NoDox0h_H3K27me3_Rep2

value: anti-H3K27me3 (Diagenode C15410069, rabbit pAb)