title: GD13 mouse uterine transcriptome, myometrial PGR deficiency 3

data_processing:
Raw reads of 101 nucleotides, paired-end filtered for quality score > 20.
Remove reads carrying adaptor sequences using cutadapt (v2.7).
Reads were mapped to the mouse genome (UCSC mm10) using STAR aligner (V2.7.0f)
Assembly: mm10
Supplementary files format and content: FPKM was calculated for each gene in each sample by using R package DESeq2 (DESeq2_1.24.0).

extract_protocol:
RNA was extracted using TRIzol according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: Gestation Day 13

value: Tissue

tag: genotype/variation

value: myometrial PGR knockout


title: F2_B3

status: Public on Sep 21 2022

type: SRA

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

country: USA

institute: Michigan State University

library_source: transcriptomic

data_processing:
Reads were trimmed for quality and adapters using TrimGalore (version 0.6.5)
Trimmed reads were mapped to Homo sapiens (human) using STAR (version 2.7.9a)
Overlapping Ensembl annotations (version 99)
Analysis was performed using edgeR-robust
Assembly: GRCh38 (hg38)
Supplementary files format and content: txt file with the raw counts per gene

molecule: total RNA

organism: Homo sapiens

source_name: Uterus

extract_protocol:
Trizol
paired-end (2 × 100 bp) RNA-sequencing on an Illumina NextSeq 6000
Kapa RNA HyperPrep kit with ribosomal re-duction, pooled, and sequenced on flowcells to yield approximately 50–60 million reads/sample.

tag: tissue

value: uterus

tag: tissue type

value: Fibroid

tag: race

value: Black


title: F2_W16

value: White


title: MC0232

city: Rochester

first: Hu

last: Li

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
Fastq files were mapped to the UCSC hg19 reference genome using STAR
gene-level counts were obtained from the alignment using HTSeq-count
Assembly: hg19
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) samples were isolated from 15 ml of whole blood before acamprosate treatment using Ficoll density gradient centrifugation. We lysed the cells in Trizol and extracted total RNA using the RNeasy mini kit (Qiagen, Valencia, CA, USA).
RNA-seq experiments were conducted by GENEWIZ using an Illumina HiSeq 4000 with eight samples in each lane using 100bp paired end index reads.

tag: cell type

value: PBMC

tag: group

value: non-relapse

tag: treatment


title: GD13 mouse uterine transcriptome, myometrial PGR deficiency 2

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

organism: Mus musculus


title: CJD_VglutCer_IP_3

city: Linköping

first: Susanne

last: Bauer

address: BKV, Cellbiologi Pl 10

department: BKV

country: Sweden

institute: Linköpings universitet

data_processing:
RNAseq data was analyzed with nf-core/rnaseq 3.0 pipeline, using default parameters. STAR/Salmon were used for alignment and quantification
Genome_build: Gencode M25 (GRCm38.p6)
Supplementary_files_format_and_content: transcript counts obtained from salmon are provided in raw_count.csv. DESeq2  (v 1.30.1) results are provided in files DEG_CJD.csv and DEG_FFI.csv. Results were obtained comparing RiboTag samples of by sample set (CJD vs. Control or FFI vs. Control).
Supplementary_files_format_and_content: raw counts per transcript for all samples, imported using tximport (v 1.18.0)
Supplementary_files_format_and_content: TPM counts per transcript for all samples, imported using tximport (v 1.18.0)
Supplementary_files_format_and_content: DGE analysis using DESeq2 (v 1.30.1) results comparing CJD and Control RiboTag samples by cell type and region.
Supplementary_files_format_and_content: DGE analysis using DESeq2 (v 1.30.1) results comparing FFI and Control RiboTag samples by cell type and region.

source_name: Cerebrum

extract_protocol:
Flash frozen brain hemispheres were homogenized and total RNA ("Input") was isolated from tissue homogenate using Trizol and purified using the Qiagen Rneasy Mini kit. For "RiboTag" samples, 12CA5 monoclonal anti-HA antibody (Roche) was coupled to protein G-coated dynabeads (Invitrogen) and incubated with tissue homogenate for 90 min to immunoprecipitate HA-tagged ribosomes and their attached mRNAs. Ribosome-bound mRNAs were isolated using Qiazol and purified using the Qiagen miRNeasy kit.
Libraries were prepared according to protovol using the Illumina TruSeq stranded mRNA kit

tag: genotype

value: CJD

tag: protocol

value: RiboTag


title: F1_W16


title: F_B2


title: MC0234


title: CJD_VglutCb_IP_2

source_name: Cerebellum


title: GD13 mouse uterine transcriptome, myometrial PGR deficiency 1


title: MC0461


title: F2_W15


title: F1_W15


title: CJD_VglutCer_IP_2


title: GD13 mouse uterine transcriptome, control 3

value: control


title: MC0216


title: CJD_VglutCb_IP_1


title: GD13 mouse uterine transcriptome, control 2


title: MC0427


title: CJD_VglutCer_IP_1


title: MC0389


title: GD13 mouse uterine transcriptome, control 1


title: F_W14


title: CJD_PV_IP_7

value: PV


title: F2_W11


title: MC0381


title: F1_W11


title: CJD_PV_total_3

value: Input


title: MC0191


title: F_W10


title: CJD_PV_IP_6


title: F_W6


title: CJD_PV_total_2


title: MyoF_B18

value: Myometrium


title: CJD_PV_IP_5


title: MyoF_B17


title: CJD_PV_IP_4


title: MyoF_B16


title: CJD_PV_IP_3


title: CJD_PV_total_1


title: MC0432


title: MC0475


title: MC0336


title: MC0188


title: CJD_PV_IP_2


title: MC0330


title: MC0238


title: MC0160


title: MyoF_B5


title: MyoF_B4


title: CJD_PV_IP_1


title: MC0196


title: MyoF_B3


title: MyoF_B15


title: CJD_GadCb_IP_6


title: MC0307


title: MyoF_B2


title: Single_worm_inf_01

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

institute: Washington State University

description:
New
Single_worm_ctr_vs_inf_DE_result.csv

data_processing:
HiSeq Control Software (HCS v2.2.68) was used for base-calling.
bcl2fastq2 Conversion Software v2.17.1 was used to convert base-calling files to fastq files and to trim adaptors.
Bowtie2 v2.3.4 was used for alignment
featureCounts from Subread v2.0.3 was used to quantify gene expression.
DESeq2 v1.34.0 was used for differential gene expression analysis.
Genome_build: UCSC ce10
Supplementary_files_format_and_content: comma-delimited text files including read counts in genes and differential gene expression

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans was cultured under standard conditions and fed E. coli strain OP50.

extract_protocol:
Individual worms were mechanically lysed using TissueLyser LT (Qiagen) without pre-processing, followed by RNA extraction using the Rneasy Mini Kit (Qiagen).
cDNA synthesis was carried out using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio). Sequencing-ready libraries were prepared using the Nextera XT DNA Library Prep Kit (Illumina).

treatment_protocol: Synchronized L1 larvae were grown on E. coli OP50 at 20⁰C until they reached young adult stage.  The worms were transferred to NGM plates seeded with P. aeruginosa PA14 for 24 hrs at 25⁰C.  The worms were then collected and washed with M9 buffer.

value: wild-type

tag: strain

tag: agent

value: infected by P. aeruginosa


title: MC0246


title: MC0405


title: MyoF_W15


title: MyoF_W16


title: CJD_GadCer_total_3


title: CJD_GadCb_total_4


title: CJD_GadCb_IP_5


title: MC0297

value: relapse


title: bulk, pbmc, mono, me3

city: New York City

first: Tim

last: Stuart

address: 101 Avenue of the Americas

institute: New York Genome Center

library_source: genomic

data_processing:
Reads were mapped to the hg38 analysis set using bwa-mem2 with default parameters (Vasimuddin et al., 2019). Output BAM files were sorted and indexed using samtools (Li et al., 2009), and bigwig files created using the deeptools bamCoverage function with the –normalizeUsing BPM option set.
Assembly: hg38
Supplementary files format and content: bigWig file containing normalized coverage for H3K27me3
Library strategy: NTT-seq

molecule: genomic DNA

source_name: Blood

extract_protocol:
Cells were purchased from AllCells. After thawing into DMEM with 10% FBS, the cells were spun down at 4°C for 5 min at 400 g and washed twice with PBS with 2% BSA. After centrifugation, the cell pellet was resuspended in 200 µL staining buffer (2% BSA and 0.01% Tween in PBS). 16% methanol-free formaldehyde (Thermo Fisher Scientific, PI28906) was added for fixation (final concentration: 0.1%) at room temperature for 5 min. The cross-linking reaction was stopped by addition of 12 µL 1.25 M glycine solution. Subsequently, cells were washed twice with PBS. The permeabilization was performed by adding isotonic lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, 1% BSA, 1× protease inhibitors) on ice for 7 min. Subsequently, 1 mL of cold wash buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors) was added, and cells were centrifuged at 800g for 5 min at 4°C.
Permeabilized cells were directly suspended with 150 µL antibody buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 2 mM EDTA, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors) with a cocktail of primary antibodies and incubated overnight on a rotator at 4°C. The next day cells were washed twice with 150 μL wash buffer to remove the remaining antibodies. The cells were then resuspended in 150 μL high salt wash buffer (20 mM HEPES pH 7.6, 300 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors) with 2.5 µL nb-Tn5 for each target of interest and incubated for 1 h on a rotator at room temperature. The cells were then washed twice with high salt wash buffer and resuspended in 50 μL tagmentation buffer (20 mM HEPES pH 7.6, 300 mM NaCl, 0.5 mM spermidine, 10 mM MgCl2, 1× protease inhibitors). The samples were incubated for 1 h at 37°C. Tagmentation steps were performed in 0.2 mL tubes to minimize cell loss. 1 µL of 0.5 M EDTA, 1 µL of 10% SDS and 1µL of 20 mg/mL Proteinase K was added to the sample, incubated at 55°C for 1 hour. DNA was extracted with Chip DNA clean & Concentrator kit (Zymo Research, D5201) following manufacturer instructions. To amplify libraries, 21 µL DNA was mixed with 2 µL of a universal i5 and a uniquely barcoded i7 primer, using a different barcode for each sample. A volume of 25 µL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72°C for 5 min (gap filling); 98°C for 30 s; 14 cycles of 98°C for 10 s and 63°C for 30 s; final extension at 72°C for 1 min and hold at 8°C. Post-PCR clean-up was performed by adding 1.1× volume of Ampure XP beads (Beckman Coulter), and libraries were incubated with beads for 15 min at RT, washed twice gently in 80% ethanol, and eluted in 30 µL 10 mM Tris pH 8.0.

value: Blood

value: PBMCs

tag: antibody


title: bulk, pbmc, multi, ac

data_processing:
Reads were mapped to the hg38 analysis set using bwa-mem2 with default parameters (Vasimuddin et al., 2019). Output BAM files were sorted and indexed using samtools (Li et al., 2009), and bigwig files created using the deeptools bamCoverage function with the –normalizeUsing BPM option set.
Assembly: hg38
Supplementary files format and content: bigWig file containing normalized coverage for H3K27ac
Library strategy: NTT-seq


title: bulk, pbmc, multi, me3


title: bulk, pbmc, mono, ac


title: single-cell, bmmc, ac

data_processing:
Reads were mapped to the hg38 analysis set using bwa-mem2 (Vasimuddin et al., 2019) with default parameters, the output sorted and indexed using samtools (Li et al., 2009), and the resulting BAM file used to create a fragment file using the Sinto package (https://github.com/timoast/sinto). We ran the sinto fragments command with the --barcode_regex "[^:]*" parameter set to extract cell barcodes from the read name. Output files were coordinate-sorted, bgzip-compressed and indexed using tabix (Li, 2011).
Assembly: hg38
Supplementary files format and content: Fragment file and index containing positions of DNA fragments per cell for H3K27ac
Library strategy: NTT-seq

source_name: Bone marrow

extract_protocol:
Cells were purchased from AllCells. After thawing into DMEM with 10% FBS, the cells were spun down at 4°C for 5 min at 400 g and washed twice with PBS with 2% BSA. After centrifugation, the cell pellet was resuspended in 200 µL staining buffer (2% BSA and 0.01% Tween in PBS). 16% methanol-free formaldehyde (Thermo Fisher Scientific, PI28906) was added for fixation (final concentration: 0.1%) at room temperature for 5 min. The cross-linking reaction was stopped by addition of 12 µL 1.25 M glycine solution. Subsequently, cells were washed twice with PBS. The permeabilization was performed by adding isotonic lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, 1% BSA, 1× protease inhibitors) on ice for 7 min. Subsequently, 1 mL of cold wash buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors) was added, and cells were centrifuged at 800g for 5 min at 4°C.
Permeabilized cells were directly suspended with 150 µL antibody buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 2 mM EDTA, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors) with a cocktail of primary antibodies and incubated overnight on a rotator at 4°C. The next day cells were washed twice with 150 μL wash buffer to remove the remaining antibodies. The cells were then resuspended in 150 μL high salt wash buffer (20 mM HEPES pH 7.6, 300 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors) with 2.5 µL nb-Tn5 for each target of interest and incubated for 1 h on a rotator at room temperature. The cells were then washed twice with high salt wash buffer and resuspended in 50 μL tagmentation buffer (20 mM HEPES pH 7.6, 300 mM NaCl, 0.5 mM spermidine, 10 mM MgCl2, 1× protease inhibitors). The samples were incubated for 1 h at 37°C. Tagmentation steps were performed in 0.2 mL tubes to minimize cell loss.  Cells were centrifuged for 5 min at 1,000g and the supernatant was discarded. Cells were resuspended with 30 µL 1× Diluted Nuclei Buffer (10x Genomics, #2000207), counted, and diluted to a concentration based on the targeted cell number. The transposed cell mix was prepared as following: 7 µL of ATAC buffer and 8 µL cells in 1× Diluted Nuclei Buffer. All remaining steps were performed according to the 10x Chromium Single Cell ATAC protocol.

value: Bone marrow

value: BMMCs


title: K562/HEK, sc, rnapii

data_processing:
Reads were mapped to the hg38 analysis set using bwa-mem2 (Vasimuddin et al., 2019) with default parameters, the output sorted and indexed using samtools (Li et al., 2009), and the resulting BAM file used to create a fragment file using the Sinto package (https://github.com/timoast/sinto). We ran the sinto fragments command with the --barcode_regex "[^:]*" parameter set to extract cell barcodes from the read name. Output files were coordinate-sorted, bgzip-compressed and indexed using tabix (Li, 2011).
Assembly: hg38
Supplementary files format and content: Fragment file and index containing positions of DNA fragments per cell for RNA Polymerase II Serine 2/5-Phos
Library strategy: NTT-seq

source_name: Immune/Kidney

extract_protocol:
Nuclei were extracted, pooled, and resuspended in 150 µL of  PBS. Then, 16% methanol-free formaldehyde (Thermo Fisher Scientific, PI28906) was added for fixation (final concentration: 0.1%) at room temperature for 3 min. The cross-linking reaction was stopped by addition of 12 µL 1.25 M glycine solution. Subsequently, nuclei were washed once with 150 µL antibody buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 2 mM EDTA, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors).
Nuclei were directly suspended with 150 µL antibody buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 2 mM EDTA, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors) with a cocktail of primary antibodies and incubated overnight on a rotator at 4°C. The next day nuclei were washed twice with 150 μL wash buffer to remove the remaining antibodies. The cells were then resuspended in 150 μL high salt wash buffer (20 mM HEPES pH 7.6, 300 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors) with 2.5 µL nb-Tn5 for each target of interest and incubated for 1 h on a rotator at room temperature. The nuclei were then washed twice with high salt wash buffer and resuspended in 50 μL tagmentation buffer (20 mM HEPES pH 7.6, 300 mM NaCl, 0.5 mM spermidine, 10 mM MgCl2, 1× protease inhibitors). The samples were incubated for 1 h at 37°C. Tagmentation steps were performed in 0.2 mL tubes to minimize cell loss.  After tagmentation, cells were centrifuged for 5 min at 1,000g and the supernatant was discarded. Cells were resuspended with 30 µL 1× Diluted Nuclei Buffer (10x Genomics, #2000207), counted, and diluted to a concentration based on the targeted cell number. The transposed cell mix was prepared as following: 7 µL of ATAC buffer and 8 µL cells in 1× Diluted Nuclei Buffer. All remaining steps were performed according to the 10x Chromium Single Cell ATAC protocol. Linear amplification was performing using the following PCR program:  (72°C for 5 min, 98°C for 30 s; 12 cycles of 98°C for 10 s, 59°C for 30 s and 72°C for 1 min; ending with hold at 15°C). The remaining steps were performed according to the 10x Genomics scATAC-seq protocol (v1.1).

value: Immune/Kidney

tag: cell line

value: RNAPII


title: single-cell, pbmc, ac


title: single-cell, pbmc, me3

data_processing:
Reads were mapped to the hg38 analysis set using bwa-mem2 (Vasimuddin et al., 2019) with default parameters, the output sorted and indexed using samtools (Li et al., 2009), and the resulting BAM file used to create a fragment file using the Sinto package (https://github.com/timoast/sinto). We ran the sinto fragments command with the --barcode_regex "[^:]*" parameter set to extract cell barcodes from the read name. Output files were coordinate-sorted, bgzip-compressed and indexed using tabix (Li, 2011).
Assembly: hg38
Supplementary files format and content: Fragment file and index containing positions of DNA fragments per cell for H3K27me3
Library strategy: NTT-seq


title: single-cell, bmmc, me3


title: MyoF_W11

value: uterus

value: White


title: K562/HEK, sc, ac


title: K562/HEK, sc, me3


title: K562, multi, rnapii

data_processing:
Reads were mapped to the hg38 analysis set using bwa-mem2 with default parameters (Vasimuddin et al., 2019). Output BAM files were sorted and indexed using samtools (Li et al., 2009), and bigwig files created using the deeptools bamCoverage function with the –normalizeUsing BPM option set.
Assembly: hg38
Supplementary files format and content: bigWig file containing normalized coverage for RNA Polymerase II Serine 2/5-Phos
Library strategy: NTT-seq

source_name: Immune

extract_protocol:
Nuclei were extracted and resuspended in 150 µL of  PBS. Then, 16% methanol-free formaldehyde (Thermo Fisher Scientific, PI28906) was added for fixation (final concentration: 0.1%) at room temperature for 3 min. The cross-linking reaction was stopped by addition of 12 µL 1.25 M glycine solution. Subsequently, nuclei were washed once with 150 µL antibody buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 2 mM EDTA, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors).
Nuclei were directly suspended with 150 µL antibody buffer (20 mM HEPES pH 7.6, 150 mM NaCl, 2 mM EDTA, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors) with a cocktail of primary antibodies and incubated overnight on a rotator at 4°C. The next day nuclei were washed twice with 150 μL wash buffer to remove the remaining antibodies. The cells were then resuspended in 150 μL high salt wash buffer (20 mM HEPES pH 7.6, 300 mM NaCl, 0.5 mM spermidine, 1% BSA, 1× protease inhibitors) with 2.5 µL nb-Tn5 for each target of interest and incubated for 1 h on a rotator at room temperature. The nuclei were then washed twice with high salt wash buffer and resuspended in 50 μL tagmentation buffer (20 mM HEPES pH 7.6, 300 mM NaCl, 0.5 mM spermidine, 10 mM MgCl2, 1× protease inhibitors). The samples were incubated for 1 h at 37°C. Tagmentation steps were performed in 0.2 mL tubes to minimize cell loss.  To stop tagmentation, 1 µL of 0.5 M EDTA, 1 µL of 10% SDS and 1µL of 20 mg/mL Proteinase K was added to the sample, incubated at 55°C for 1 hour. DNA was extracted with Chip DNA clean & Concentrator kit (Zymo Research, D5201) following manufacturer instructions. To amplify libraries, 20 µL DNA was mixed with 2.5 µL of a universal i5 and a uniquely barcoded i7 primer, using a different barcode for each sample. A volume of 25 µL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72°C for 5 min (gap filling); 98°C for 30 s; 14 cycles of 98°C for 10 s and 63°C for 30 s; final extension at 72°C for 1 min and hold at 8°C. Post-PCR clean-up was performed by adding 1.1× volume of Ampure XP beads (Beckman Coulter), and libraries were incubated with beads for 15 min at RT, washed twice gently in 80% ethanol, and eluted in 30 µL 10 mM Tris pH 8.0.

value: Immune


title: K562, mono, rnapii


title: K562, multi, me3


title: K562, multi, ac


title: K562, mono, ac


title: CJD_GadCer_IP_5

value: CJD

value: RiboTag


title: CJD_GadCer_IP_4


title: MC0273

value: PBMC


title: MC0397


title: CJD_GadCb_total_3

value: Input


title: MyoF_W14

value: Myometrium


title: MyoF_W10


title: MyoF_W6


title: MC0270


title: CJD_GadCb_IP_4


title: CJD_GadCer_IP_3


title: CJD_GadCb_total_2


title: MyoF_W3


title: MC0332


title: MC0301


title: Placental Tissue, Preeclampsia, Subject4 [PE4]

city: Wenzhou

first: Meng

last: Zhou

address: 270 Xueyuan Xi Road

country: China

institute: Wenzhou Medical University

data_processing:
Fastp was applied to remove low-quality reads and adapters of the raw sequencing reads
Sequence reads were aligned to mature human miRNA  index (miRbase v.22, GRCh38)
miRDeep2.pl command was executed to quantify known miRNAs
Assembly: GRCh38, miRbase v.22
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Placental Tissue

extract_protocol:
Total RNAs were purified from approximately 100 mg of tissue from the central regions of each placenta, using Qiagen RNeasy Purification Kit (Hilden, Germany). The qualitative assessment of RNA samples (28S/18S, 1.8-2.2; RIN, 9.5-10) were performed by Bioanalyzer (Agilent).
A total amount of 1μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using TruSeq miRNA Sample Prep Kit for Illumina. Manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Placental Tissue

tag: disease status

value: preeclamptic

tag: Sex

value: female


title: MC0200

value: relapse


title: Placental Tissue, Preeclampsia, Subject2 [PE2]


title: CJD_GadCb_IP_3


title: Placental Tissue, Preeclampsia, Subject3 [PE3]


title: Placental Tissue, Preeclampsia, Subject5 [PE5]


title: MC0363


title: CJD_GadCer_total_2


title: K562, mono, me3


title: MC0211


title: MC0194


title: CJD_GadCer_IP_2


title: Placental Tissue, Preeclampsia, Subject1 [PE1]


title: RPMI 8226_shHDAC1_replicate3

city: Tokushima

first: Takeshi

last: Harada

state: Tokushima

address: 3-18-15 Kuramoto-cho

department: Hematology, Endocrinology and Metabolism

country: Japan

institute: Tokushima University Graduate School of Biomedical Sciences

data_processing:
Sequenced reads were aligned to the reference human genome (hg19) using RNA-specific STAR aligner.
Reads was normalized using DESeq.
Differential gene expression analysis to compare HDAC1 knockdown samples with control samples was performed using DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include transcripts per million (TPM) values for each sample

source_name: Multiple myeloma cell line

growth_protocol: RPMI 8226 cells were maintained in RPMI-1640 medium supplemented with 10%  fetal bovine serum in 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA was then treated with TURBO DNA-free reagents (Thermo Fisher Scientific).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.

treatment_protocol: RPMI 8226 cells were transduced with control vector of Luciferase or HDAC1 shRNA by lentiviral system. The transduced cells were selected using puromycin for 48 hr.

value: RPMI 8226

tag: knockdown


title: RPMI 8226_shLuc_replicate3

value: shLuc


title: RPMI 8226_shLuc_replicate2


title: RPMI 8226_shHDAC1_replicate1


title: RPMI 8226_shHDAC1_replicate2


title: MC0224


title: RPMI 8226_shLuc_replicate1


title: CJD_GadCb_IP_2


title: Input-seq, pool 2

data_processing:
50nt sequence reads were identified by the Sequencing Service (using Illumina’s Genome Analyzer 2).
Reads were mapped to the mouse genome mm10 using  Bowtie with unique mapping and up to 2 mismatches for each read (-m 1 -v 2)
Assembly: mm10
Supplementary files format and content: Bigwig files were generated using bedGraphToBigWig from UCSC.

extract_protocol:
Chromatin samples were prepared by Active Motif Services - Factor Path assays
Libraries were prepared by Active Motif Services - Factor Path assays

tag: Stage

value: Gestation Day 13

value: Tissue


title: Input-seq, pool 1


title: CJD_GadCer_total_1


title: MC0195


title: The PGR occupancy profile in pooled mouse uterine tissues at GD13, pool 2

value: Anti-PGR antibody (sc-7208, Santa Cruz Biotechnology, Dallas, TX)


title: Placental Tissue, Normal, Subject4 [NC4]

value: normotensive


title: CJD_GadCer_IP_1


title: MC0416


title: Placental Tissue, Normal, Subject3 [NC3]


title: Placental Tissue, Normal, Subject2 [NC2]


title: CJD_GadCb_total_1


title: MC0219


title: CJD_GadCb_IP_1


title: H3K27ac histone mark profile in pooled mouse uterine tissues at GD13

value: Anti-H3K27ac antibody (cat # 39133, Active Motif, Caslsbad, CA)


title: MC0368


title: Placental Tissue, Normal, Subject1 [NC1]


title: FFI_SST_IP_6

value: FFI

value: SST


title: Placental Tissue, Normal, Subject5 [NC5]


title: MC0309


title: MC0277


title: MC0406


title: F4KD_C: Fbxo4 knock-down rep 3

city: Cleveland

first: J Alan

last: Diehl

state: Ohio

address: 2109 Adelbert Rd. SOM Wood/W402

department: Department of Biochemistry

institute: Case Western Reserve University

data_processing:
Raw image data file from high-throughput sequencing (Illumina PE150) was transformed to Sequenced Reads by CASAVA 1.8 base recognition (Base Calling)
To eliminate low quality reads or reads with adaptors the following filtering conditions has been applied: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). ClusterProfiler R package was utilized to test the statistical enrichment of differential expression genes in KEGG pathway, Gene Ontology (GO) and Reactome.
Genome_build: Homo_sapiens_(GRCh38/hg38)
Supplementary_files_format_and_content: raw count and FPKM (txt)
Supplementary_files_format_and_content: mapping summary (txt)

source_name: WM983B cells

growth_protocol: WM983B cell lines were cultured in the media containing: 80% MCDB153 medium, 20% Leibovitz L-15, 2% fetal bovine serum (FBS), 1.68 mM CaCl2 and Penicillin-Streptomycin

extract_protocol:
2.5 x 10^6 cells were plated 24 hours befofore extraction of RNA with RNeasy kit (Qiagen, cat# 74104)
First strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library was obtained by PCR amplification and purification of PCR products by AMPure XP beads

treatment_protocol: Fbxo4 knock-down was induced by lentiviral infection (shRNA purchased from Dharmacon-Horizon, Clone ID: TRCN0000034321) followed by 72h negative selection with 0.5mg/ml puromcycin. Control cells were infected with empty lentivius.

value: melanoma

value: lentivirus encoding anti-Fbxo4 shRNA


title: FFI_SST_IP_5

value: RiboTag


title: FFI_SST_IP_4


title: THP1, control, 1

city: Seoul

first: Hong-Tae

last: Park

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

data_processing:
For the processing of bacterial transcriptome profile, sequence reads were mapped onto the reference genome of MAP (NC_002944.2) using Bowtie (v1.2.2) with a maximum insert size of 1000 bp and two maximum mismatches after trimming 3 bp at the 3’ ends. Subsequently, SAM output files generated from Bowtie were transformed to BAM format using SAMtools (http://samtools.sourceforge.net/). The differential gene expression was analyzed using the DESeq2 R package.
For the processing of human transcriptome profile, the relative abundances of genes were measured in Read Count using StringTie.
Statistical analysis was performed to find DEGs using the estimates of abundances for each gene in samples. Data were then log2-transformed and subjected to TMM normalization. Statistical significance of the differential expression data was determined using exactTest using edgeR and fold change in which the null hypothesis was that no difference exists among groups.
False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.
Assembly: GRCh37/hg19, NC_002944.2
Supplementary files format and content: Text files include FPKM values for each Sample

source_name: Human monocyte cell line

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen, Germany). Illumina TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Briefly, removal of rRNA in the total RNA was conducted using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina, Inc., San Diego, CA, USA) and the NEBNext rRNA Depletion kit (Bacteria) (NEB). After the depletion of rRNA, the remaining RNA was fragmented into small pieces. The cleaved RNA fragments were copied into first strand cDNA using SuperScript II reverse transcriptase (Invitrogen) and random primers, followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. After the ligation of adapters to the cDNA, the products are then purified and enriched with PCR.
Dual RNA-seq

value: monocyte

tag: infection

value: uninfected


title: FFI_SST_IP_3


title: The PGR occupancy profile in pooled mouse uterine tissues at GD13, pool 1

tag: tissue


title: MC0289

value: PBMC


title: THP1, control, 2


title: FFI_SST_total_3

value: Input


title: 7d_rep1

type: RNA

city: Nantong

first: Yun

last: Gu

state: Jiangsu

address: 19 Qixiu Road

department: Jiangsu Key Laboratory of Neuroregeneration

institute: Nantong University

description: Gene expression in Schwann cells after co-cultured with DRG neurons for 7 days

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US

organism: Rattus norvegicus

source_name: Schwann cells, co-culture with DRG neuron7d, replicate 1

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Rat Schwann cells and dorsal root ganglion (DRG) neurons were isolated and cocultured in DMEM-HG medium with 10% FBS, and allowed to attach overnight. The next day, the media was replaced with DRG growth medium for 2 d to allow the Schwann cells to repopulate the neurites and then switched to the DMEM medium supplemented with 50 ng/ml NGF, ITS (Sigma), and 0.2% bovine serum albumin (BSA) (Sigma) for about 4 d to initiate basal lamina formation, then the premyelinated cocultures were maintained in DMEM medium containing 15% FBS, 50 ng/ml NGF and 50 μg/ml L-ascorbic acid (AA) (Sigma) for 2-3 w.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: In the co-cultures, appropriate SCs (Myelinating SCs at different stages) were selected on a computer-controlled inverted microscope with a stage incubator that creates a physiological atmosphere for the preparations (Cell Observer, Zeiss, Oberkochen, Germany); their coordinates were recorded to serve as a reference. During selection, any SCs exhibiting signs of stress, such as vacuoles, blebs, deformed membranes, were excluded.   For laser capture microdissection (LCM), we used a Leica laser microdissection systems (LMD7000, Leica). The myelinating SCs at different stages were dissected by UV laser (laser power set to 2.2-3.2) and attached to CapSure LCM caps with help of infrared laser (power set to 80%). Caps were collected in 0.5 ml eppendorf tubes containing 100μl of RNAlater buffer (QIAGEN) and stored upside down at -80°C until RNA isolation.

value: Schwann cells

tag: time point

value: Nerve


title: 7d_rep3

source_name: Schwann cells, co-culture with DRG neuron7d, replicate 3


title: MC0185

value: relapse


title: 7d_rep2

source_name: Schwann cells, co-culture with DRG neuron7d, replicate 2


title: WT_C: control- empty vector rep 3

value: empty lentiviral vector


title: FFI_SST_IP_2


title: WT_B: control- empty vector rep 2


title: F4KD_A: Fbxo4 knock-down rep 1


title: FFI_SST_total_1


title: FFI_SST_IP_1


title: MC0257


title: MC0212


title: WT_A: control- empty vector rep 1


title: F4KD_B: Fbxo4 knock-dwon rep 2


title: MC0308


title: FFI_SST_total_2


title: B14_WK3_aSYN_V

city: Boston

first: Christine

last: Cheng

state: Massachusetts

address: 24 Cummington Mall

department: Biology

institute: Boston University

description: 10X Genomics 3' V3.1

data_processing:
Each sequencing library was demultiplexed based on the sample index read to generate FASTQ files for the RNA pair-end reads using Cell Ranger V3.1.0.
Gene-cell barcode matrices for RNA count data were generated using 10X genomics CellRanger V3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: 10X Genomics MEX UMI-corrected raw count matrix (.mtx) and associated gene and barcode (.tsv) files

source_name: human induced pluripotent stem cell derived neurons and astrocytes

growth_protocol: Human induced pluripotent stem cell derived neural progenitor cells  (Stem Cell Technologies) were differentiated to neurons (hiNCs) and astrocytes (hiACs) and combined in microwells at a 1:1 ratio to form self-aggregating spheroids (asteroids).

extract_protocol:
A single cell suspension of asteroid cultures was prepared by Accutase dissociation and 20 uM filtration.
scRNA-seq libraries were prepared following 10X Genomics Chromium Single Cell 3’ V3 scRNA-seq method.
scRNA-seq, 10X Genomics 3'

treatment_protocol: hiNCs were treated with 0.04 mg/mL oligomeric tau or 1 ug/mL PFF-aSYN to induce pathology in oTAU and aSYN samples respectivly. Asteroids were treated for 72 hrs with 1 uM PU-H71 before timepoint collection in drug treated samples.

value: WK3 aSYN V


title: MC0320


title: MC0470


title: B14_WK3_oTAU_V

description: 10X Genomics 3' V3.1

value: WK3 oTAU V


title: B14_WK3_Control_V

description: 10X Genomics 3' V3.1

value: WK3 Control V


title: MC0296


title: FFI_VglutCb_IP_4


title: MC0243


title: FFI_VglutCer_total_3


title: 3d_rep1

description: Gene expression in Schwann cells after co-cultured with DRG neurons for 3 days

source_name: Schwann cells, co-culture with DRG neuron3d, replicate 1


title: 3d_rep3

source_name: Schwann cells, co-culture with DRG neuron3d, replicate 3


title: 21d_rep1

description: Gene expression in Schwann cells after co-cultured with DRG neurons for 21 days

source_name: Schwann cells, co-culture with DRG neuron21d, replicate 1


title: 21d_rep3

source_name: Schwann cells, co-culture with DRG neuron21d, replicate 3


title: FFI_VglutCb_total_3

source_name: Cerebellum


title: 3d_rep2

source_name: Schwann cells, co-culture with DRG neuron3d, replicate 2


title: 1d_rep3

description: Gene expression in Schwann cells after co-cultured with DRG neurons for 1 days

source_name: Schwann cells, co-culture with DRG neuron1d, replicate 3


title: 21d_rep2

source_name: Schwann cells, co-culture with DRG neuron21d, replicate 2


title: H3K27me3_CIN_d35_rep3

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

description: H3K27me3 CIN Cut-Tag replicate 3

data_processing:
Library strategy: CUT&TAG
Raw reads were processed using AIAP (v1.1) to peform QC, alignment, bigwig file generation, and peak calling
Genome_build: hg38
Supplementary_files_format_and_content: bigwig signal density and macs2 peak calls

source_name: embryonic stem cells

growth_protocol: Embryonic stem cells were mainatined in mTeSR media on Matrigel coated cultureware

extract_protocol:
For CUT and TAG genomic DNA was amplified after tagmentation and purified using AMPure XP beads. For ChIP DNA was purified using AMPure XP beads.
For CUT and TAG samples with unique dual-end indexes were pooled in equimolar concentrations and were sequenced on the NovaSeq-6000 sequencer with the S4 flow cell as 2 x 150 bp paired-end reads at a depth of 10 million. For ChIP library preparation and sequencing were performed using the HiSeq3000 sequencer to obtain at least 30 M single end 50 base pair reads per sample reads per sample

treatment_protocol: Embryonic stem cells were specified as medial ganglionic eminence (hMGE) progenitor and then further differentiated into human cortical interneurons (hcIN)

value: cortical interneuron

tag: stem cell source

value: H9 hESC

tag: passage

tag: timepoint


title: exclude_3

source_name: Cerebrum

value: exclude

value: FFI

tag: cell type


title: 1d_rep2

source_name: Schwann cells, co-culture with DRG neuron1d, replicate 2


title: human_74

city: Neuherberg

first: Sophie

last: Tritschler

address: Ingolstädter Landstrasse 1

country: Germany

institute: Helmholtz Zentrum Munich

data_processing:
The 10X Genomics core computational software Cellranger v.2.0 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). For read 2 150bp were considered for alignment.
For QC, filtering, normalization and batch correction the scanpy python package v.1.4-1.6 and anndata v0.6-0.7, a python implementation of Combat and the R package scran were used. Scripts for preprocessing with detailed descriptions are available here: https://github.com/theislab/2022_Tritschler_pancreas_cross_species
Assembly: hg19, susscrofa
Supplementary files format and content: anndata (annotated data matrix) object saved in h5ad-file format. Raw file contains raw count data for all cells. Processed file contains raw and normalized count data of filtered and annotated cells.

molecule: polyA RNA

source_name: Single cells of human pancreatic islets

extract_protocol:
For single-cell suspension of human and pig islets, 60 islets were hand-picked into a 1.5 ml Eppendorf tube, pelleted (280g, 1 min), washed with PBS (minus Mg or Ca, Gibco) and digested with Tryp-LE (Gibco) at 37 °C for 12 min. During the incubation step with Tryp-LE, islets were mechanically disaggregated with a 1ml pipet tip every 2–3 min. The digestive reaction was then stopped by adding FACS-buffer (PBS, 2% FCS, 2mM EDTA) and cells were pelleted (280g, 3 min). Cells were stained with trypan blue to visualize dead cells and counted with a hemocytometer.
Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 (PN #120237) from 10x Genomics. Libraries were sequenced on the HiSeq4000 (Illumina) with 150bp paired-end sequencing of read2.
RNA Seq (10X Genomics)

tag: source tissue

value: pancreas

tag: developmental day

value: adult

tag: treatment


title: FFI_VglutCb_total_2

data_processing:
RNAseq data was analyzed with nf-core/rnaseq 3.0 pipeline, using default parameters. STAR/Salmon were used for alignment and quantification
Genome_build: Gencode M25 (GRCm38.p6)
Supplementary_files_format_and_content: transcript counts obtained from salmon are provided in raw_count.csv. DESeq2  (v 1.30.1) results are provided in files DEG_CJD.csv and DEG_FFI.csv. Results were obtained comparing RiboTag samples of by sample set (CJD vs. Control or FFI vs. Control).
Supplementary_files_format_and_content: raw counts per transcript for all samples, imported using tximport (v 1.18.0)
Supplementary_files_format_and_content: TPM counts per transcript for all samples, imported using tximport (v 1.18.0)
Supplementary_files_format_and_content: DGE analysis using DESeq2 (v 1.30.1) results comparing CJD and Control RiboTag samples by cell type and region.
Supplementary_files_format_and_content: DGE analysis using DESeq2 (v 1.30.1) results comparing FFI and Control RiboTag samples by cell type and region.

tag: genotype

tag: protocol


title: H3K27me3_CIN_d35_rep2

description: H3K27me3 CIN Cut-Tag replicate 2


title: H3K27me3_NPC_d15_rep3

description: H3K27me3 NPC Cut-Tag replicate 3

value: medial ganglionic eminence neuronal precursor


title: H3K27me3_CIN_d35_rep1

description: H3K27me3 CIN Cut-Tag replicate 1


title: human_63


title: 1d_rep1

source_name: Schwann cells, co-culture with DRG neuron1d, replicate 1


title: 14d_rep3

description: Gene expression in Schwann cells after co-cultured with DRG neurons for 14 days

source_name: Schwann cells, co-culture with DRG neuron14d, replicate 3


title: human_61


title: FFI_VglutCer_total_2


title: human_24


title: H3K27me3_NPC_d15_rep2

description: H3K27me3 NPC Cut-Tag replicate 2


title: 14d_rep2

source_name: Schwann cells, co-culture with DRG neuron14d, replicate 2


title: FFI_VglutCb_IP_3

value: RiboTag


title: 0d_rep3

description: Gene expression in Schwann cells after co-cultured with DRG neurons for 0 days

source_name: Schwann cells, co-culture with DRG neuron0d, replicate 3


title: H3K27me3_NPC_d15_rep1

description: H3K27me3 NPC Cut-Tag replicate 1


title: FFI_VglutCb_total_1


title: FFI_VglutCer_IP_3


title: human_22


title: H3K27me3_ESC_d0_rep4

description: H3K27me3 ESC Cut-Tag replicate 4

value: embryonic stem cells


title: SCC9-parental

city: Shanghai

first: Chao

last: Lou

address: No. 639 Zhizaoju Road

institute: Shanghai Jiaotong University

data_processing:
Basecalls performed using CASAVA version 1.8
mRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
mRNAs were detected and annotated with CIRI software
Genome_build: hg19
Supplementary_files_format_and_content: mRNA Expression Profiling.xlsx (FPKMs, counts)

source_name: Tumor

extract_protocol:
Total RNA was harvested using Trizol reagent and then used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNextÂ® Ultraâ¢ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturerâs instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: Tumor

tag: cell line

value: SCC9-parental cells


title: SCC9-seeded

value: SCC9-seeded cells


title: FFI_VglutCb_IP_2


title: H3K27me3_ESC_d0_rep3

description: H3K27me3 ESC Cut-Tag replicate 3


title: 48hr shCDK9 gilteritinib3

city: Columbus

first: Pu

last: Zhang

address: 1258 Bunkerhill Blvd, AptB

institute: Ohio State University

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterREmoval v2.2.0 to remove sequencing adapters
Reads were aligned against the human genome using HISAT2 v2/0/6 using default parameters
Unaligned deconaminome reads were aligned against the human genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M25
Transcript counts were DESeq2 size normalized
Genome_build: GRCh38
Supplementary_files_format_and_content: A txt counts table (DESeq2 normalized) generated using Subread FeatureCounts

growth_protocol: shCDK9, shDHODH and scrambled shRNA-stable MOLM13 cells were grown in RPMI1640+10% FBS.

extract_protocol:
The Clontech SMARTer v4 kit (Takara Bio USA, Inc., Mountain View, CA) was used for extracting and preamplifying samples.
Library construction with the Nextera XT DNA Library Prep Kit (Illumina, Inc., San Diego, CA).

treatment_protocol: Cells were treated with 1) DMSO 2) 8nM gilteritinib for in triplicates for 48 hr and 96 hr.

value: gilteritinib

tag: time


title: H3K27me3_ESC_d0_rep2

description: H3K27me3 ESC Cut-Tag replicate 2


title: FFI_VglutCer_IP_2

extract_protocol:
Flash frozen brain hemispheres were homogenized and total RNA ("Input") was isolated from tissue homogenate using Trizol and purified using the Qiagen Rneasy Mini kit. For "RiboTag" samples, 12CA5 monoclonal anti-HA antibody (Roche) was coupled to protein G-coated dynabeads (Invitrogen) and incubated with tissue homogenate for 90 min to immunoprecipitate HA-tagged ribosomes and their attached mRNAs. Ribosome-bound mRNAs were isolated using Qiazol and purified using the Qiagen miRNeasy kit.
Libraries were prepared according to protovol using the Illumina TruSeq stranded mRNA kit


title: FFI_VglutCer_IP_4


title: 48hr shCDK9 gilteritinib2


title: H3K27me3_ESC_d0_rep1

description: H3K27me3 ESC Cut-Tag replicate 1


title: 48hr shCDK9 gilteritinib1


title: FFI_VglutCb_total

value: Input


title: 14d_rep1

description: Gene expression in Schwann cells after co-cultured with DRG neurons for14 days

source_name: Schwann cells, co-culture with DRG neuron14d, replicate 1

value: Schwann cells

value: Nerve


title: 0d_rep1

source_name: Schwann cells, co-culture with DRG neuron 0d, replicate 1


title: FFI_VglutCb_IP_1


title: 0d_rep2

source_name: Schwann cells, co-culture with DRG neuron0d, replicate 2


title: ATAC-seq from H1 induced Trophoblast Stem Cells in TSC-m medium, w/o induction H1T-rep2_S4

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were trimmed with Trim using python script (https://github.com/TheJacksonLaboratory/ATAC-seq/blob/master/auyar/pyadapter_trim.py)
Reads were aligned to hg38 human genome using Bowtie2 with the parameter -X2000 (allowing fragments up to 2 kb to align).
Peaks were identified using MACS2 callpeak function, with the following parameters: --nomodel --shift -100 --extsize 200.
Assembly: hg38
Supplementary files format and content: bed files, MACS2 callpeak output

source_name: naïve-derived Trophoblast Stem Cells

growth_protocol: Primed hESCs were grown in KSR/FGF medium on irradiated MEFs;  Naïve/Primed/Embryo-derived TSC cells were grown in TSC-m or TSC-a medium, as indicated. Naive/Primed-derived TSCs were used for analysis 10-20 passages after conversion from PSCs.

extract_protocol:
Cells were trypsinized and counted, 50,000 cells were centrifuged at 500g for 3 min, followed by a wash using 50 μl of cold PBS and centrifugation at 500g for 3 min.
Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. Next, the pellet was resuspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C and immediately put on ice. Directly afterwards, the sample was purified using a Qiagen MinElute kit. Following purification, the library fragments were amplified using custom Nextera PCR primers 1 and 2 for a total of 12 cycles. Following PCR amplification, the libraries were purified using a QiagenMinElute Kit and sequenced.

value: ndTSC

tag: media conditions

value: TSC-m, w/o induction medium

tag: batch


title: ATAC-seq from WIBR3 induced Trophoblast Stem Cells in TSC-m medium W3A-rep2_S6

value: TSC-m


title: ATAC-seq from WIBR3 primed Embryonic Stem Cells W3primed-rep2_S8

source_name: primed human Embryonic Stem Cells

value: Primed hESCs

value: Primed


title: ATAC-seq from WIBR3 primed Embryonic Stem Cells W3primed-rep1_S7


title: CHD2_CIN_d35_rep2

description: CHD2 CIN Cut-Tag replicate 2

value: cortical interneuron

value: H9 hESC


title: 48hr shCDK9 DMSO3

value: DMSO


title: FFI_VglutCer_total_1

value: FFI


title: 48hr shCDK9 DMSO2


title: ATAC-seq from H1 induced Trophoblast Stem Cells in TSC-m medium, w/o induction H1T-rep1_S3


title: CHD2_CIN_d35_rep1

description: CHD2 CIN Cut-Tag replicate 1


title: ATAC-seq from H1 induced Trophoblast Stem Cells in TSC-m medium H1A-rep2_S2


title: 48hr shCDK9 DMSO1


title: FFI_VglutCer_IP_1

value: RiboTag


title: ATAC-seq from WIBR3 induced Trophoblast Stem Cells in TSC-m medium W3A-rep1_S5


title: ATAC-seq from H1 induced Trophoblast Stem Cells in TSC-m medium H1A-rep1_S1


title: CHD2_CIN_d35_rep3

description: CHD2 CIN Cut-Tag replicate 3


title: CHD2_NPC_d15_rep3

description: CHD2 NPC Cut-Tag replicate 3

value: medial ganglionic eminence neuronal precursor


title: ATAC-seq from bTS11 Trophoblast Stem Cells in TSC-m medium bTS11_edTSC_M_S2

source_name: embryo-derived Trophoblast Stem Cells

value: TSC


title: 48hr Scrambled gilteritinib 3

value: scrambled shRNA


title: FFI_PV_IP_5

value: PV


title: CHD2_NPC_d15_rep2

description: CHD2 NPC Cut-Tag replicate 2


title: 48hr Scrambled gilteritinib 2

value: gilteritinib


title: 48hr Scrambled gilteritinib1


title: FFI_PV_IP_4


title: 48hr Scrambled DMSO3


title: CHD2_ESC_d0_rep2

description: CHD2 ESC Cut-Tag replicate 2

value: embryonic stem cells


title: FFI_PV_total_2

value: Input


title: FFI_PV_total_3


title: CHD2_ESC_d0_rep3

description: CHD2 ESC Cut-Tag replicate 3


title: 48hr Scrambled DMSO2


title: ATAC-seq from WIBR3 induced Trophoblast Stem Cells in TSC-a medium WIBR3_pdTSC_A_S8

source_name: primed-derived Trophoblast Stem Cells

value: pdTSC

value: TSC-a


title: ATAC-seq from WIBR3 primed Embryonic Stem Cells WIBR3_REP_S7


title: CIN CHD2-KO H3K27Ac Cut-Tag replicate 4

data_processing:
Library strategy: CUT&TAG
Raw reads for ATACseq and Cut&Tag samples were processed using AIAP (v1.1) for trimming, alignment, and bigWig generation
Raw reads for RNAseq samples were quality trimmed using cutadapt (v3.4) and aligned using STAR (v2.5.4b). Aligned reads were quantified using featureCounts (v1.4.6-p4) from the subreads package.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig density file for ATACseq and Cut&Tag. featureCount text file for RNAseq.

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (Takara Bio). For CUT and TAG genomic DNA was amplified after tagmentation and purified using AMPure XP beads.
RNA-seq library preparation and Illumina sequencing was performed using the SMARTer Ultra Low RNA kit (Takara-Clontech) per the manufacturer’s instructions. Paired-end 150 bp reads were obtained using an Illumina NovaSeq-6000 sequencer with the S4 flow cell, to a depth of ~30 M reads per sample. For CUT and TAG samples with unique dual-end indexes were pooled in equimolar concentrations and were sequenced on the NovaSeq-6000 sequencer with the S4 flow cell as 2 x 150 bp paired-end reads at a depth of 10 million reads per sample

treatment_protocol: Embryonic stem cells were specified to hMGE and then further differentiated into hcIN

tag: iPSc source


title: CHD2_ESC_d0_rep1

description: CHD2 ESC Cut-Tag replicate 1


title: FFI_PV_IP_3


title: ATAC-seq from H1 induced Trophoblast Stem Cells in TSC-m medium H1_pdTSC_M_S6

value: TSC-m


title: FFI_PV_IP_2


title: DHODH gilteritinib3

value: shDHODH


title: 48hr Scrambled DMSO1


title: CIN CHD2-KO H3K27Ac Cut-Tag replicate 3


title: ATAC-seq from bTS11 Trophoblast Stem Cells in TSC-a medium bTS11_edTSC_A_S1


title: DHODH gilteritinib2


title: CHD2_NPC_d15_rep1

description: CHD2 NPC Cut-Tag replicate 1


title: FFI_PV_total_1


title: exclude_2

value: exclude


title: FFI_PV_IP_1


title: CIN CHD2-KO H3K27Ac Cut-Tag replicate 2

value: cortical interneuron


title: ATAC-seq from H1 induced Trophoblast Stem Cells in TSC-a medium H1_pdTSC_A_S5


title: ATAC-seq from CT30 Trophoblast Stem Cells in TSC-m medium CT30_edTSC_M_S4


title: ATAC-seq from WIBR3 induced Trophoblast Stem Cells in TSC-m medium WIBR3_pdTSC_M_S9


title: CIN CHD2-KO H3K27Ac Cut-Tag replicate 1

value: H9 hESC


title: ATAC-seq from CT30 Trophoblast Stem Cells in TSC-a medium CT30_edTSC_A_S3


title: FFI_GadCb_IP_5

source_name: Cerebellum


title: DHODH DMSO3

value: DMSO


title: FFI_GadCb_IP_4

value: FFI


title: NPC CHD2-KO H3K27Ac Cut-Tag replicate 4

source_name: embryonic stem cells


title: DHODH DMSO2


title: NPC CHD2-KO H3K27Ac Cut-Tag replicate 3


title: DHODH DMSO1


title: wholeME1

city: Mahasset

first: Andrew

last: Shih

state: NY

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

description:
10x Genomics
Shih_endo_cell_data.tsv
metadata.xlsx

library_source: transcriptomic single cell

data_processing:
Samples were converted from raw bcl files to gene by cell matrices using CellRanger 6.0 aligned to 10x Genomics' GRCh38-3.0.0 reference. Individuals were demultiplexed via Demuxlet [42] using genotypes taken from SNPs on the Illumina GSAv3 genotyping array, run on DNA prepared from neutrophils isolated from ME. The thresholds in Demuxlet were adjusted to the expected doublet rate and those marked as doublets were removed.
Assembly: GRCh38-3.0.0
Supplementary files format and content: h5 files

source_name: wholeME

extract_protocol:
Endometriosis, symptomatic, and control subjects collected their ME using an ‘at home’ ME collection kit for 4-8 hours on the day of their heaviest menstrual flow (typically day 1 or 2 of the cycle) with a menstrual cup (provided by DIVA International), except for one subject who collected ME using a novel menstrual collection sponge. After collection, ME was shipped priority overnight at 4◦ C to the laboratory for processing. ME collected from menstrual cups was mixed 1:1 with DMEM for processing. For the saturated menstrual collection sponge, ME tissue was collected after rinsing the sponges with PBS to collect cells and tissue. Whole (unfractionated) ME (2.5-10ml) was digested with Collagenase I (1mg/ml, Worthington Biochemical Corporation, Lakewood, NJ) and DNase I (0.25mg/ml, Worthington Biochemical Corporation) at 37°C for 10-30 min using the gentleMACSTM Tissue Octo Dissociator (Miltenyi Biotec, Cambridge, MA) using C tubes and Program 37CMulti_E_01 (31 min). After digestion, the sample was sieved over a 70μ filter and washed with DMEM 10%FBS to neutralize digestion enzymes; the flow through was sieved over a 40μ filter and washed with DMEM 10%FBS. After collecting the single cells (from the flow through) following centrifugation (350xg for 5 min), Neutrophils were removed using the EasySepTM HLA Chimerism Whole Blood CD66b Positive Selection Kit (STEMCELL, Cambridge, MA), according to the manufacturer’s protocol. The neutrophil pellet was frozen at -80°C and used as a source of subject DNA for genotyping (see below). The resultant cells were depleted of red blood cells using the EasySepTM RBC Depletion Reagent (STEMCELL), according to the manufacturer’s protocol, and then washed and subjected to density gradient centrifugation using Ficoll-Paque PLUS (Sigma-Aldrich, St. Louis, MO) to collect mononuclear cells, according to manufacturer’s directions. To collect ME-tissue, whole ME (2.5-10ml) was sieved over a 70μ filter and washed with DMEM; the ME-tissues trapped on the filter was collected and digested with Collagenase I (1mg/ml, Worthington Biochemical Corporation, Lakewood, NJ) and DNase I (0.25mg/ml, Worthington Biochemical Corporation) at 37°C for 10 min and processed as described above for whole ME, except without a density gradient centrifugation step. The resultant whole ME cells were enumerated, and viability was assessed using ViaStainTM AOPI Staining Solution and the Nexcelom Cellometer (Lawrence, MA). Preparations with >80% viability were processed for scRNA-Seq. Cells were immediately fixed in methanol for scRNA-Seq, as described by Chen for peripheral blood mononuclear cells [41]). Briefly, cells were washed and resuspended in a 200μl Ca ++ and Mg++-free PBS, followed by dropwise addition of chilled 100% methanol (800μl, final 80% w/v). Fixed cells were stored at -20°C for 20min and then stored at -80°C until used for scRNA-Seq.
Methanol-fixed cells were removed from -80°C and placed on ice for 5 min before centrifugation (1000xg for 5 min). Methanol-PBS supernatant was completely removed and cells were rehydrated in 0.04% BSA + 1mM DTT + 0.2 U/ul RNase Inhibitor in 3X SSC (saline sodium citrate buffer solution) Buffer (Sigma). An aliquot of fixed cells was stained with Trypan Blue and visualized under the microscope. The cells were counted and pooled from different donors at equal ratios, filtered using 35μ strainer (Falcon), recounted and brought up to a final conc. Of 2,000 cells/μl and proceeded immediately for GEM generation and barcoding on a 10X Chromium using Next GEM 3’ v3.1 reagents (10X Genomics). Libraries were constructed following 10X Genomics’ recommendations and quality was assessed on a High Sensitivity DNA chip on a BioAnalyzer 2100 (Agilent) before loading (1.8 pM) and sequencing on an Illumina Nextseq 500 using a High Output kit v2.5 (150 cycles).
3’ RNA-seq

value: wholeME


title: FFI_GadCer_IP_6

source_name: Cerebrum

value: RiboTag


title: FFI_GadCer_IP_5


title: DHODH gilteritinib1


title: NPC CHD2-KO H3K27Ac Cut-Tag replicate 1

value: medial ganglionic eminence neuronal precursor


title: wholeME3


title: NPC CHD2-KO H3K27Ac Cut-Tag replicate 2


title: Scrambled gilteritinib 3

value: scrambled shRNA


title: FFI_GadCb_total_4


title: Scrambled gilteritinib 1


title: exclude_1


title: CIN wt H3K27Ac Cut-Tag replicate 4


title: wholeME2


title: MEtissue6

source_name: MEtissue

value: MEtissue


title: CIN wt H3K27Ac Cut-Tag replicate 3


title: Scrambled gilteritinib 2

value: gilteritinib


title: FFI_GadCb_IP_3


title: MEtissue7


title: MEtissue4


title: CIN wt H3K27Ac Cut-Tag replicate 2


title: Scrambled DMSO3


title: FFI_GadCer_total_3


title: MEtissue5


title: Scrambled DMSO2


title: CIN wt H3K27Ac Cut-Tag replicate 1


title: FFI_GadCer_IP_4


title: Scrambled DMSO1


title: NPC wt H3K27Ac Cut-Tag replicate 4


title: MEtissue3


title: FFI_GadCb_total_3


title: MEtissue1


title: MEtissue2


title: TS543_CTRL

city: Heidelberg

first: Sevin

last: Turcan

address: INF 460

institute: NCT

data_processing:
The RNAseq data were analysed with the DKFZ/ODCF RNAseq workflow (https://github.com/DKFZ-ODCF/RNAseqWorkflow,v1.2.22-6).
FASTQ reads for individual samples were aligned by a 2 pass alignment using the STAR aligner v2.5.2b. Reads were aligned to a STAR index generated from the 1000 genomes assembly, gencode 19 gene models. Duplicate marking of the resultant main alignment file was done with sambamba v0.6.5. BAM indexes were generated using sambamba. Quality control analysis was performed using the samtools flagstat command (samtools v1.6), and the rnaseqc tool.
Featurecounts was used to perform gene specific read counting over exon features based on the gencode 19 gene models. Strand unspecific counting was used.
Feature counts were converted to Deseq abundance measurements using Deseq2 package.
Genome_build: hg19 (1KGRef_PhiX)
Supplementary_files_format_and_content: Matrix table with normalized Deseq abundance measurements for every gene in each individual cell line

source_name: brain glioma

growth_protocol: hNSC, TS603, S24, TS600 and TS543 cells were seeded in a concentration of 5 x 105 cells/well in 6-well dishes in triplicates and harvested 48 h after seeding.

extract_protocol:
Total mRNA from biological triplicates of CTRL/TRIM67 was extracted using the QIAGEN RNeasy RNA isolation kit according to manufacturer’s protocol.
RNA-seq libraries were created with TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Stable cell lines were created by viral transduction with pLVX-empty and pLVX-Flag-TRIM67 plasmids. TRIM67 was then constitutively expressed by the transduced cells.

value: brain

value: glioblastoma cells

value: IDH WT, chromosome 1p-19q intact

value: control


title: NPC wt H3K27Ac Cut-Tag replicate 2


title: TS543_TRIM67

value: TRIM67 overexpression


title: TS600_TRIM67


title: FFI_GadCb_total_2

value: Input


title: FFI_GadCb_total_1


title: NPC wt H3K27Ac Cut-Tag replicate 3


title: FFI_GadCb_IP_2


title: FFI_GadCb_IP_1


title: wholeME_Metissue

source_name: wholeME/Metissue

value: wholeME/Metissue


title: CIN CHD2-KO ATACseq replicate 4

data_processing:
Raw reads for ATACseq and Cut&Tag samples were processed using AIAP (v1.1) for trimming, alignment, and bigWig generation
Raw reads for RNAseq samples were quality trimmed using cutadapt (v3.4) and aligned using STAR (v2.5.4b). Aligned reads were quantified using featureCounts (v1.4.6-p4) from the subreads package.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig density file for ATACseq and Cut&Tag. featureCount text file for RNAseq.

value: cortical interneuron


title: WIBR3_primed_2

description: Embryonic Stem Cells

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
STAR software version 2.5.3a was used to align reads to human GRCh38 reference genome (2013), using the following flags: --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --twopassMode Basic --outSAMstrandField intronMotif.
Read count values were estimated with HTSeq V0.7.2 software over all aligned reads using GRCh38 general feature format (GFF), with the following flags: -a 10 -s no -t exon -i gene_id. Mitochondrial and ribosomal genes were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: HTSeq counts of all samples

source_name: WIBR3 primed Embryonic Stem Cells

growth_protocol: Primed hESCs were grown in KSR/FGF medium on irradiated MEFs; Human fibroblasts were grown in DMEM/FBS. Naïve/Primed/Embryo-derived TSC cells were grown in TSC-m or TSC-a medium, as indicated. Naive/Primed-derived TSCs were used for analysis 10-20 passages after conversion from PSCs.

extract_protocol:
Total RNA was extracted from indicated cell lines at 50% confluency with Trizol reagent.
RNA was next utilized for RNA-Seq by ScriptSeq Preparation Kit v2 (Illumina) according to manufacturer’s instruction

value: Primed hESCs

value: Primed

tag: induction medium

value: no


title: TS600_CTRL

tag: tissue


title: CIN CHD2-KO ATACseq replicate 3

value: H9 hESC


title: H1_primed_2

description: Embryonic Stem Cells

source_name: H1 primed Embryonic Stem Cells


title: S24_TRIM67


title: FFI_GadCer_IP_3

value: FFI

value: RiboTag


title: WIBR3_ndTSC_m_ni_2

description: Naïve-derived Trophoblast Stem Cells

source_name: Naïve WIBR3 hES derived Trophoblast Stem Cells, converted by direct application of TSC-m medium, grown in TSC-m medium

value: iTSC

value: TSC-m


title: CIN CHD2-KO ATACseq replicate 2


title: S24_CTRL


title: NPC wt H3K27Ac Cut-Tag replicate 1

value: medial ganglionic eminence neuronal precursor


title: TS603_TRIM67

value: brain

value: oligodendroglioma cells

value: IDH mutant, chromosome 1p-19q co-deleted


title: FFI_GadCer_total_2


title: H1_ndTSC_m_ni_2

description: Naïve-derived Trophoblast Stem Cells

source_name: Naïve H1 hES derived Trophoblast Stem Cells, converted by direct application of TSC-m medium, grown in TSC-m medium


title: CIN CHD2-KO ATACseq replicate 1


title: FFI_GadCer_IP_2


title: TS603_CTRL

value: control


title: NPC CHD2-KO ATACseq replicate 4


title: H1_ndTSC_m_i_2

description: Naïve-derived Trophoblast Stem Cells

source_name: Naïve H1 hES derived Trophoblast Stem Cells, converted with the use of induction medium, grown in TSC-m medium

value: yes


title: FFI_GadCer_IP_1


title: NPC CHD2-KO ATACseq replicate 3


title: FFI_GadCer_total_1

value: Input


title: Human_Fibroblast_2_1

description: Fibroblasts

source_name: Human fibroblasts, replication 2

value: GM07982 fibroblasts from Coriell repository

value: Fibroblasts

value: DMEM/FBS


title: NPC CHD2-KO ATACseq replicate 2


title: Human_Fibroblast_1_1

description: Fibroblasts

source_name: Human fibroblasts, replication 1

value: GM05131 fibroblasts from Coriell repository


title: WIBR3_primed_1

description: Embryonic Stem Cells

value: Primed hESCs

value: Primed

value: no


title: NPC CHD2-KO ATACseq replicate 1

value: H9 hESC


title: E12.5_WT_IgG_R1.fq.gz

city: Beijing

first: Zhang

last: shuangfeng

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

institute: Institute of Zoology, Chinese Academy of Sciences

description: CUT&Tag

data_processing:
Library strategy: CUT&TAG
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie2 (v.2.4.1).
MACS2 (v.2.2.7.1) was used to call peaks (-g mm -q 0.01 -f BAM) relative to input sample. MAnorm (v.1.2.0) was then used for quantitative comparison of ChIP-Seq data.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: wig files were generated using bamcoverage function of DeepTools (v.3.4.0).
Supplementary_files_format_and_content: tab-delimited text files. Peak annotation was performed using ChIPseeker (v.1.22.1) at gene level and promoter regions was defined as +/- 3000bp of TSS

source_name: Forebrain tissue

extract_protocol: EED DNA libraries were prepared for sequencing using standard BGISEQ-500 protocols. Other DNA libraries were prepared from CUT&Tag protocol and using standard NovaSeq protocols.

tag: strain

value: wild type

value: forebrain

value: untreated


title: CIN wt ATACseq replicate 4

value: cortical interneuron


title: PARP3KO_LN229_1 [FSDR4]

city: Illkirch

first: Françoise

last: DANTZER

address: 300 boulevard S. Brant

country: France

institute: CNRS

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed using cutadapt 1.10 in order to remove adaptors and low-quality sequences and reads shorter than 40 bp were removed for further analysis. Remaining reads were mapped to Homo sapiens rRNA and ERCC Spike-In sequences using bowtie 2.2.8 and reads mapped to those sequences were removed for further analysis. Remaining reads were aligned to hg38 assembly of Homo sapiens with STAR 2.5.3a.
Gene quantification was performed with htseq-count 0.6.1p1, using “union” mode and Ensembl 91 annotations. Differential gene expression analysis was performed using DESeq2 1.16.1. Bioconductor R package on previously obtained counts (with default options). P-values were adjusted for multiple testing using the Benjamini and Hochberg method.
Genome_build: hg38
Supplementary_files_format_and_content: htseq-count, DESeq2 1.16.1 output

growth_protocol: Cells were grown in MEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS,  Dominique Dutscher) and 1% gentamicine (Gibco). The cell lines were maintained at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using the RNeasy Mini-Kit (Qiagen) following the manufacturer’s instructions.
Total RNA-Seq libraries were generated from 1000ng of total RNA using TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: proliferating human glioblastoma cell line


title: PARP3KO_LN229_2 [FSDR5]


title: CIN wt ATACseq replicate 3


title: WIBR3_ndTSC_m_i_2

description: Naïve-derived Trophoblast Stem Cells

source_name: Naïve WIBR3 hES derived Trophoblast Stem Cells, converted with the use of induction medium, grown in TSC-m medium

value: iTSC

value: TSC-m


title: WIBR3_pdTSC_a_1

description: primed-derived Trophoblast Stem Cells

source_name: WIBR3 primed-derived Trophoblast Stem Cells in TSC-a medium

value: TSC-a

value: yes


title: E12.5_WT_RNA-Pol2_R1.fq.gz

description: CUT&Tag


title: H1_primed_1

description: Embryonic Stem Cells


title: PARP3KO_LN229_3 [FSDR6]


title: hNSC_TRIM67

source_name: neural stem cells

value: brain

value: ES-derived neural stem cells

value: IDH WT, chromosome 1p-19q intact

value: TRIM67 overexpression


title: E12.5_WT_H3K27ac_R1.fq.gz

description: CUT&Tag


title: PARP3WT_LN229_3 [FSDR3]


title: CIN wt ATACseq replicate 2

source_name: embryonic stem cells


title: hNSC_CTRL

value: control


title: H1_pdTSC_a_1

description: primed-derived Trophoblast Stem Cells

source_name: H1 primed-derived Trophoblast Stem Cells in TSC-a medium


title: WIBR3_pdTSC_m_1

description: primed-derived Trophoblast Stem Cells

source_name: WIBR3 primed-derivedTrophoblast Stem Cells in TSC-m medium


title: E12.5_cKO_IgG_R1.fq.gz

description: CUT&Tag

value: EedcKO


title: PARP3WT_LN229_1 [FSDR1]


title: H1_pdTSC_m_1

description: primed-derived Trophoblast Stem Cells

source_name: H1 primed-derived Trophoblast Stem Cells in TSC-m medium


title: PARP3WT_LN229_2 [FSDR2]


title: NPC wt ATACseq replicate 4

value: medial ganglionic eminence neuronal precursor


title: NPC wt ATACseq replicate 3

value: H9 hESC


title: CT30_edTSC_a_1

description: embryo-derived Trophoblast Stem Cells

source_name: CT30 embryo-derived Trophoblast Stem Cells in TSC-a medium

value: TSC


title: Input siDDX5/17 R3

city: Lyon

first: Cyril

middle: F

last: Bourgeois

address: 46 Allée d'Italie

department: LBMC

institute: ENS de Lyon

description: Replicate 3

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: Neuroblastoma SH-SY5Y cell line (ECACC)

growth_protocol: Cells were cultured in 4,5 g/L Glucose DMEM/F-12 (ThermoFischer Scientific) supplemented with 10% (v/v) fetal bovine serum (ThermoFischer Scientific), and 2 mM L-Glutamine (ThermoFischer Scientific) in 5% CO2 at 37°C.

extract_protocol:
Cells were cross-linked (1% formaldehyde), harvested, lysed and sonicated (Covaris S220 ultrasonicator). Chromatin (40 µg per antibody) was diluted and precleared on Protein A/G Dynabeads for 30 min at 4°C under rotation. Beads were removed and 1% of chromatin was taken apart as Input material. Antibodies were added to chromatin and incubated overnight at 4°C under constant mixing, before being bound to Protein A/G Dynabeads for 5h.   Immunoprecipitated material was washed once with Low Salt buffer, once with High Salt Buffer, once with LiCl Buffer and twice with Tris/EDTA buffer, before being eluted and reverse crossed-linked  overnight at 65°C on Thermomixer (Eppendorf) in the presence of 200 mM NaCl and 20 µg proteinase K (Roche). DNA was then purified by phenol extraction and ethanol precipitation, and quantified for library preparation.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + --- cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: Cells were transfected for 48h with siRNAs at a final concentration of 20 nM with lipofectamine RNAimax (ThermoFischer Scientific).

tag: transfected sirna

value: siRNA anti-DDX5/DDX17

tag: extract

value: Chromatin extract (input)


title: E12.5_cKO_RNA-Pol2_R1.fq.gz

description: CUT&Tag

value: forebrain

value: untreated


title: IP RNAPII siDDX5/17 R3

description: Replicate 3

value: RNA Pol II IP (F12 antibody)


title: CT30_edTSC_m_1

description: embryo-derived Trophoblast Stem Cells

source_name: CT30 embryo-derived Trophoblast Stem Cells in TSC-m medium

value: TSC-m


title: Input Ctrl R3

description: Replicate 3

value: Negative control siRNA anti-luciferase


title: NPC wt ATACseq replicate 2

tag: passage


title: E12.5_cKO_H3K27me3_R1.fq.gz

description: CUT&Tag


title: E12.5_cKO_H3K27ac_R1.fq.gz

description: CUT&Tag


title: NPC wt ATACseq replicate 1

tag: cell type


title: 4-2

city: little rock

first: Dongzheng

last: Gai

state: AR

address: 4301 W Markham St

institute: UAMS

data_processing:
The raw sequencing data (fastq files) were preprocessed using CellRanger software (10x Genomics) version 6 with reference genome of Mus musculus version mm10 to demultiplex for cell and transcript and generate count table.
The count table were load in to R through Seurat version 4 package for further analysis.
Principal component analysis (PCA) was then performed on significantly variable genes of the remained high-quality cells. The results of individual sample were used for data integration across samples using reciprocal PCA method to minimize technical differences between samples.
Then the nitration results were used as input for clustering using Louvain algorithm with multilevel refinement and Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP). The gene specific markers of each cluster were identified using the FindMarkersAll function with MAST method test statistics. The expression pattern of selected gene markers across cell cluster were plot as a heat map to assess the quality of cell clustering result.
To visualize some of gene markers simultaneously in kernel joint density estimatiscon, Nebulosa package was used. Based on the kernel joint density of Adgr1 and Fcgr3, we sub select cells that have high value of the kernel joint density for subclsutering analysis to study the cellular heterogeneity of Macrophage cells. Gene-set enrichment analysis of marker genes was performed on Gene Ontology annotation using piano package.
Genome_build: mmp10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Mice bone marrow mononuclear cells

extract_protocol:
The RNA were prepared using the Chromium Single Cell 3′ Reagent Kits (v3.1) follow the standard protocol.
The libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v3.1) follow the standard protocol.

value: Mice bone marrow mononuclear cells

tag: age

tag: agent


title: 4-4


title: bTS11_edTSC_a_1

description: embryo-derived Trophoblast Stem Cells

source_name: bTS11 embryo-derived Trophoblast Stem Cells in TSC-a medium

value: TSC-a

value: yes


title: 4-1


title: CIN wt ATACseq replicate 1

value: cortical interneuron


title: bTS11_edTSC_m_1

description: embryo-derived Trophoblast Stem Cells

source_name: bTS11 embryo-derived Trophoblast Stem Cells in TSC-m medium


title: B3_WK3_oTAU_V

description: 10X Genomics 3' V2

source_name: human induced pluripotent stem cell derived neurons and astrocytes

tag: treatment

value: WK3 oTAU V


title: 2-2

value: PBS


title: IP RNAPII siDDX5/17 R2

description: Replicate 2


title: Input Ctrl R2

description: Replicate 2


title: B6_WK3_Control_V

description: 10X Genomics 3' V2

value: WK3 Control V


title: B6_WK3_oTAU_V

description: 10X Genomics 3' V2


title: 2-1


title: IP RNAPII Ctrl R2

description: Replicate 2


title: NPC CHD2-KO RNAseq replicate 2

value: medial ganglionic eminence neuronal precursor


title: B3_WK3_Control_V

description: 10X Genomics 3' V2


title: IP RNAPII siDDX5/17 R1

description: Replicate 1


title: 1-3


title: NPC CHD2-KO RNAseq replicate 1

value: H9 hESC


title: Input siDDX5/17 R1

description: Replicate 1


title: CIN CHD2-KO RNAseq replicate 2


title: 1-2

value: Control


title: CIN wt RNAseq replicate 4


title: 1-1


title: CIN CHD2-KO RNAseq replicate 1


title: Input siDDX5/17 R2

description: Replicate 2

value: siRNA anti-DDX5/DDX17


title: B10_WK2_Control_V

description: 10X Genomics 3' V3

value: WK2 Control V


title: RANKL+CST6 3

data_processing:
Utilizing Salmon version 1.2.1 – for quantifying expression at gene level.
Utilizing DESeq2 – for importing salmon data, normalization and differential expression.
Genome_build: Gencode M25 (GRCm38.p6)
Supplementary_files_format_and_content: Matrix table with normalized gene counts for genes/samples

source_name: Mice primary macrophages

growth_protocol: Bone marrow macrophages were cultured in α-MEM containing 10% FBS and 10ng/ml M-CSF.

extract_protocol:
Cells were processed for RNA extraction using the Quick-DNA/RNA FFPE Miniprep Kit with on-column DNase digestion for the RNA preps (catalog # D7003; Zymo Research, Irvine CA, USA).
Sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep (catalog # 20020595; Illumina, San Diego CA, USA) with the IDT for Illumina Unique Dual indices (catalog # 20022371; Illumina, San Diego CA, USA).

treatment_protocol: Bone marrow macrophages were cultured in α-MEM containing 10% FBS and 10ng/ml M-CSF for 3 days. Then the macropgaes were treated with RANKL with or without recombinant CST6 for 48h.

value: Bone marrow cells


title: CIN wt RNAseq replicate 3


title: Input Ctrl R1

description: Replicate 1

value: Chromatin extract (input)


title: B10_WK1_oTAU_V

description: 10X Genomics 3' V3

data_processing:
Each sequencing library was demultiplexed based on the sample index read to generate FASTQ files for the RNA pair-end reads using Cell Ranger V3.1.0.
Gene-cell barcode matrices for RNA count data were generated using 10X genomics CellRanger V3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: 10X Genomics MEX UMI-corrected raw count matrix (.mtx) and associated gene and barcode (.tsv) files

value: WK1 oTAU V


title: RANKL+CST6 2


title: NPC CHD2-KO RNAseq replicate 3


title: IP RNAPII Ctrl R1

description: Replicate 1

value: RNA Pol II IP (F12 antibody)


title: NPC CHD2-KO RNAseq replicate 4


title: CIN wt RNAseq replicate 2


title: RANKL+CST6 1


title: B10_WK1_Control_V

description: 10X Genomics 3' V3

value: WK1 Control V


title: B11_WK3_oTAU_PU

description: 10X Genomics 3' V3

value: WK3 oTAU PU


title: CIN wt RNAseq replicate 1


title: NPC wt RNAseq replicate 4


title: Tl_800ppb_rep1

city: Taipei

first: Jui-Feng

last: Tsai

address: No. 1, Sec. 1, Ren'Ai Rd,

department: Graduate Institute of Toxicology

country: Taiwan

institute: National Taiwan University

data_processing:
Bioinformatic analysis was performed by Azenta Life Sciences, Inc. (Chelmsford, MA).
Fastqc for reads quality check
Cutadapt for adaptor trimming
STAR for alignment to reference genome
RSeQC for post-alignment quality control
edgeR for normalization to CPM
Assembly: Danio rerio GRCz11
Supplementary files format and content: The CSV file (*_readcount.csv) contains raw read counts of each gene for each sample.
Supplementary files format and content: The CSV file (CPM.csv) includes log2CPM values of each gene among all the samples.

organism: Danio rerio

source_name: embryo

extract_protocol:
RNA extraction was performed with TRIzol reagent according to manufacturer’s instruction (Invitrogen, Waltham, MA). RNA quality assessment was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturers’ protocol.
cDNA library construction was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturers’ protocol.

treatment_protocol: Wild type zebrafish embryos were exposed to 0, 200, and 800 ppb TlNO3 from 6 to 48 hpf.

value: embryo

tag: genotype

value: Wild type

value: Tl 800 ppb

value: 6 to 48 hpf


title: Tl_800ppb_rep2


title: RANKL3


title: RANKL1


title: B11_WK3_oTAU_V

description: 10X Genomics 3' V3

extract_protocol:
A single cell suspension of asteroid cultures was prepared by Accutase dissociation and 20 uM filtration.
scRNA-seq libraries were prepared following 10X Genomics Chromium Single Cell 3’ V3 scRNA-seq method.
scRNA-seq, 10X Genomics 3'

value: WK3 oTAU V


title: NPC wt RNAseq replicate 3


title: RANKL2


title: Tl_200ppb_rep3

value: Tl 200 ppb


title: B11_WK3_Control_V

description: 10X Genomics 3' V3

value: WK3 Control V


title: NPC wt RNAseq replicate 2

value: medial ganglionic eminence neuronal precursor

value: H9 hESC


title: Control 3


title: Tl_200ppb_rep2


title: Control 2


title: Tl_200ppb_rep1

data_processing:
Bioinformatic analysis was performed by the sequencing core of department of medical research, National Taiwan University Hospital.
Fastqc for reads quality check
Cutadapt for adaptor trimming
STAR for alignment to reference genome
RSeQC for post-alignment quality control
edgeR for normalization to CPM
Assembly: Danio rerio GRCz11
Supplementary files format and content: The CSV file (*_readcount.csv) contains raw read counts of each gene for each sample.
Supplementary files format and content: The CSV file (CPM.csv) includes log2CPM values of each gene among all the samples.

extract_protocol: RNA extraction was performed with TRIzol reagent according to manufacturer’s instruction (Invitrogen, Waltham, MA). RNA quality assessment and cDNA library construction were performed by the sequencing core of department of medical research, National Taiwan University Hospital according to manufacturers’ protocol.


title: Tl_0ppb_rep5

value: Tl 0 ppb


title: ARPE19 cancer cell progession line - ARPE19 rep 2

city: Fort Collins

first: Erin

last: Osborne Nishimura

state: CO

address: 1870 Campus Delivery, 200 W. Lake St.

department: Biochemistry and Molecular Biology

institute: Colorado State University

data_processing:
Samples were assessed for quality and trimmed for adapter, primer, and polyX sequences by fastp (v 0.20.0) (Chen 2017; PMID: 30423086)
Trimmed reads were aligned separately to either the hg38 genome or to transgenic sequences using hisat2 (v 2.1.0) (Kim 2017; PMID: 31375807).
The number of reads associated with each gene model was tabulated for the human genome annotation (hg38_pc_20200113_UCSC_compatible.gtf.gz) using featureCounts (v 1.6.4) (Liao 2014; PMID: 24227677).
samtools (v 1.9) (Li 2009; PMID: 19505943), DeepTools (bamCoverage v 3.2.0) (Ramírez 2016; PMID: 27079975), and UCSC Kent Utilities were used to transform alignments into formats suitable for viewing on UCSC Genome Browser (Kent 2002; PMID: 12045153) or IGV (v 2.9.0) (Robinson 2011; PMID: 21221095).
RNA-seq count data were filtered for detected genes (> 10 counts across all samples) and analyzed using DESeq2 (v 1.28.1) (Love 2014; PMID: 25516281) with default settings in the R Environment (v 4.0.3, BiocManager, v 1.30.10).
The raw counts (210215_raw_counts.txt), normalized counts (210215_norm_counts.txt), and normalized/variance-stabilized/log-transformed counts (210215_RStabilized_log_counts.txt) are provided.
Genome_build: human genome, hg38
Supplementary_files_format_and_content: .bw files were generated using bamCoverage, part of the DeepTools package
Supplementary_files_format_and_content: merged.bw files were merged by replicate using UCSC Kent Utilities
Supplementary_files_format_and_content: counts tables were generated from featureCounts tabultion and then processed within DESeq2

source_name: Human retinal pigment epitheial cell line

growth_protocol: Cells were grown adherently in DMEM/F12 (Thermo 11330) supplemented with 10% FBS and antibiotic-antimycotic (Thermo 15240062)

extract_protocol:
Total RNA was extracted from ~2 million cells using an RNeasy mini kit (Qiagen 74104). Each replicate was isolated from a freshly thawed cryovial that had been passaged twice prior to extraction.
mRNA was prepared for sequencing using the NEB Next Ultra II Directional Library Prep Kit for Illumina (NEB E7760S) and Poly(A) Magnetic Isolation Module (NEB E7490S).
Libraries of a median 200 - 400 bp length were generated and sequenced at 2 x 150 bp on a NovaSeq 6000 to a read depth of roughly 50 – 100 million reads.

tag: transfection

value: no transfection

tag: cell line pathway

tag: disease state

value: not transformed


title: NPC wt RNAseq replicate 1


title: Control 1

value: Bone marrow cells


title: B11_WK3_Control_PU

description: 10X Genomics 3' V3

value: WK3 Control PU


title: Tl_0ppb_rep4

tag: time


title: B10_WK2_oTAU_V

description: 10X Genomics 3' V3

value: WK2 oTAU V


title: B11_WK2_Control_PU

description: 10X Genomics 3' V3

value: WK2 Control PU


title: B11_WK2_oTAU_V

description: 10X Genomics 3' V3


title: ARPE19 cancer cell progession line - AKTmyr rep 2

value: pbabe-hTERT+p53DD (Addgene plasmid # 11128); pbabe-cyclinD1+CDK4R24C (Addgene plasmid # 11129); pBabe-myr-HA-Akt, (Addgene plasmid # 15294)

value: PI3K-AKT pathway

value: transformed


title: Tl_0ppb_rep3

value: embryo

value: Wild type


title: Adenine_3

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

description: JF5 A03

data_processing:
Quality of the raw sequencing files was examined using the FastQC (v0.11.9) software package.
Sequences were aligned to the reference mouse genome GRCm38.p6 primary assembly version and the corresponding annotation GTF file vM25 from GENCODE using the STAR software (v2.7.6a).
Gene-level read counts were quantified and assembled using the R package Rsubread (v2.2.6).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: expression_read_counts.tsv, a table with tab-separated values for the raw read counts for every gene and every sample.

source_name: Heart

growth_protocol: Group housing with a 12h light- and dark-cycle, free access to water and food. Male 129/Sv mice were studied. The CKD group was fed with a diet containing 0.15% adenine for 13 weeks. The control group received a standard diet for 13 weeks. CKD onset and progression upon adenine diet were confirmed by increasing plasma creatinine and urea levels over time (to ~6-7-fold increase at endpoint) as well as strong kidney fibrosis as detected by increased COL1 protein expression, renal Sirius Red staining and AFOG staining. Furthermore, tubular injury was detected in all adenine-fed mice as revealed by PAS-stained histological slides.

extract_protocol:
RNA was extracted by using peqGOLD TriFast Kit (Peqlab) according to manufacturer's instructions
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions

treatment_protocol: Cardiac tissue was rinsed with ice-cold PBS and was snap-frozen in liquid nitrogen directly after organ explantation, after which it was stored at -80°C until RNA extraction.

value: Tissue

value: chronic kidney disease

value: adenine diet

value: Heart


title: Tl_0ppb_rep2

value: 6 to 48 hpf


title: Adenine_4

description: JF5 A04


title: B11_WK2_Control_V

description: 10X Genomics 3' V3

value: WK2 Control V


title: B11_WK2_oTAU_PU

description: 10X Genomics 3' V3

value: WK2 oTAU PU


title: B11_WK1_oTAU_V

description: 10X Genomics 3' V3

value: WK1 oTAU V


title: Adenine_2

description: JF5 A02


title: Tl_0ppb_rep1

value: Tl 0 ppb


title: B11_WK1_Control_V

description: 10X Genomics 3' V3

value: WK1 Control V


title: ARPE19 cancer cell progession line - MekDD rep 2

value: pbabe-hTERT+p53DD (Addgene plasmid # 11128); pbabe-cyclinD1+CDK4R24C (Addgene plasmid # 11129); pBabe-Puro-MEK-DD (Addgene plasmid # 15268)

value: MAPK pathway

value: weakly transformed


title: O3_330WO_72_1

city: Perugia

first: Lorenzo

last: Brunetti

address: Piazzale Menghini 8/9

country: Italy

institute: University of Perugia

data_processing:
FastQ files were aligned to the hg19 genome using HISAT version 2.1.0
Quantification performed using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: fpkm text file

source_name: OCI-AML3 cells

growth_protocol: OCI-AML3 cells were cultured in complete RPMI FBS 10%

extract_protocol:
RNA was purified using the Zymo Quick-RNA Microprep Kit
Illumina TruSeq stranded mRNA protocol

tag: cell ine

tag: tissue source

value: Blood and bone marrow

value: AML cell line

value: Selinexor 72 hours short treatment


title: Sham_4

description: JF5 S04

value: healthy

value: control diet


title: Adenine_1

description: JF5 A01

value: Tissue

value: chronic kidney disease


title: THP1, MAP, Dual, 1

city: Seoul

first: Hong-Tae

last: Park

address: 1, Gwanak-ro

institute: Seoul National University

data_processing:
For the processing of bacterial transcriptome profile, sequence reads were mapped onto the reference genome of MAP (NC_002944.2) using Bowtie (v1.2.2) with a maximum insert size of 1000 bp and two maximum mismatches after trimming 3 bp at the 3’ ends. Subsequently, SAM output files generated from Bowtie were transformed to BAM format using SAMtools (http://samtools.sourceforge.net/). The differential gene expression was analyzed using the DESeq2 R package.
For the processing of human transcriptome profile, the relative abundances of genes were measured in Read Count using StringTie.
Statistical analysis was performed to find DEGs using the estimates of abundances for each gene in samples. Data were then log2-transformed and subjected to TMM normalization. Statistical significance of the differential expression data was determined using exactTest using edgeR and fold change in which the null hypothesis was that no difference exists among groups.
False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.
Assembly: GRCh37/hg19, NC_002944.2
Supplementary files format and content: Text files include FPKM values for each Sample

organism:
Homo sapiens
Mycobacterium avium subsp. paratuberculosis K-10

source_name: Human monocyte cell line

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen, Germany). Illumina TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Briefly, removal of rRNA in the total RNA was conducted using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina, Inc., San Diego, CA, USA) and the NEBNext rRNA Depletion kit (Bacteria) (NEB). After the depletion of rRNA, the remaining RNA was fragmented into small pieces. The cleaved RNA fragments were copied into first strand cDNA using SuperScript II reverse transcriptase (Invitrogen) and random primers, followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. After the ligation of adapters to the cDNA, the products are then purified and enriched with PCR.
Dual RNA-seq

tag: cell line

value: monocyte

tag: infection

value: MAP


title: ARPE19 cancer cell progession line - T53D4 rep 3

value: pbabe-hTERT+p53DD (Addgene plasmid # 11128); pbabe-cyclinD1+CDK4R24C (Addgene plasmid # 11129)

value: T53D4 primed cell line

value: not transformed


title: ARPE19 cancer cell progession line - RasV12 rep 3

value: pbabe-hTERT+p53DD (Addgene plasmid # 11128); pbabe-cyclinD1+CDK4R24C (Addgene plasmid # 11129); pWZL-H-RasV12 (Addgene plasmid # 18749)

value: RAS pathway

value: transformed


title: Eluate, 100 nM

city: Berkeley

first: Timothy

middle: J

last: Eisen

state: CALIFORNIA

address: Stanley Hall

institute: UC Berkeley

description: mRNA display

data_processing:
Alignment of paired-end FASTQ files using Kallisto (Bray et al., 2016).
Supplementary files format and content: Tab-delimited read count file, as output from the aligner.

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Sample 64

extract_protocol:
mRNA display was performed on a library of variants. Peptides were selected based on their ability to bind to a His6-tagged HR1 peptide, which was purified with Ni-NTA beads.
Peptide-mRNA fusions were reverse-transcribed using Superscript III (ThermoFisher) and oligo-dT(20-mer) as an RT primer. After precipitation, cDNA was PCR-amplified, agarose-gel purified, and sequenced.

tag: fraction

value: Eluate

tag: hr1 concentration


title: Sham_3

description: JF5 S03

tag: tissue

tag: strain

value: Heart


title: Sham_2

description: JF5 S02


title: O3_330_72_1

value: Blood and bone marrow

tag: cell type

value: Selinexor 72 hours continous treatment


title: ARPE19 cancer cell progession line - AKTmyr rep 3

value: pbabe-hTERT+p53DD (Addgene plasmid # 11128); pbabe-cyclinD1+CDK4R24C (Addgene plasmid # 11129); pBabe-myr-HA-Akt, (Addgene plasmid # 15294)

value: PI3K-AKT pathway


title: ARPE19 cancer cell progession line - ARPE19 rep 3

value: no transfection


title: ARPE19 cancer cell progession line - RasV12 rep 2


title: ARPE19 cancer cell progession line - T53D4 rep 2


title: O3_330_72_0

value: AML cell line


title: THP1, MAP, Dual, 2


title: Eluate, 10 nM

description: mRNA display

source_name: Sample 46


title: Sham_1

description: JF5 S01

value: Tissue

value: healthy

value: control diet


title: ARPE19 cancer cell progession line - MekDD rep 3

value: pbabe-hTERT+p53DD (Addgene plasmid # 11128); pbabe-cyclinD1+CDK4R24C (Addgene plasmid # 11129); pBabe-Puro-MEK-DD (Addgene plasmid # 15268)

value: MAPK pathway

value: weakly transformed