title: A549 sgM16-2 input

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

institute: China Pharmaceutical University

description:
Total RNA
10mM ZnCl2
sg16E7_In

data_processing:
For Ribo-Seq data analysis, cutadapt (v.2.8) was used to trim the adapters and low quality sequences with --match-read-wildcards -a NNNNNNNNNNAGATCGGAAGAGCAC -q 20 -e 0.1 -O 3 -m 25 -M 35 -U 10 -A AGATCGGAAGAGCGT -A AGATCGGAAGAGCGTC -A AGATCGGAAGAGCGTCG -A AGATCGGAAGAGCGTCGT -A AGATCGGAAGAGCGTCGTG -A AGATCGGAAGAGCGTCGTGT parameters.
For RNA-Seq data analysis, cutadapt (v.2.8) was used to trim the adapters and low quality sequences with --match-read-wildcards -a NNNNNNNNNNAGATCGGAAGAGCAC -q 20 -e 0.1 -O 3 -m 20 -U 10 -A AGATCGGAAGAGCGT -A AGATCGGAAGAGCGTC -A AGATCGGAAGAGCGTCG -A AGATCGGAAGAGCGTCGT -A AGATCGGAAGAGCGTCGTG -A AGATCGGAAGAGCGTCGTGT parameters.
The remaining reads were trimmed again with same parameters. Reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie2 (v2.2.5) software. Then the clean reads were aligned to human genome (GRCh38) with STAR aligner (v2.7.5c) with --outFilterMultimapNmax 10 --alignEndsType EndToEnd --outFilterMismatchNmax 2 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --outFilterIntronMotifs RemoveNoncanonicalUnannotated parameters and gencode genes (gencode.v38.annotation.gtf) transcriptome annotation. Then mapped reads were quantified using featureCounts (v2.0.1) with -t exon parameter. The TPM (Transcripts Per Kilobase of exonmodel per Million mapped reads) was used for downstream analysis. Translation efficiency (TE) was calculated by (TPM of Ribo-seq)/(TPM of RNA-seq) and only genes with an RNA-seq TPM greater than 1 were used in the translation efficiency calculation. TE < 0.5 or > 2 were considered as translation-downregulated or translation-upregulated genes. For read coverage on each transcript, reads were aligned to human transcriptome sequences using bowtie(v1.3.0) with -m 1 -v 2 --best --strata parameters. For each gene, the mRNA with longest CDS was selected. In the case of equal CDS length, the longest transcript was used.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx format files include samples TPM values

growth_protocol: NSCLC cells were cultured overnight in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin to achieve 70-80% confluency. Cells were incubated with fresh medium for 2 h and 100ug/mL Cycloheximide treatment for 5 min before harvesting.

extract_protocol:
Input RNA was extracted with TRIzol LS followed by chemical fragmentation. Ribo-seq samples were produced by RNase I digestion followed by RNA extraction using TRIzol LS.
40-60nt region for input and 30nt for ribo-seq were selected according to 15% polyacrylamide TBE-urea gel separation. Desired RNA species were excised and soaked overnight followed by ethanol precipitation. The purified RNA was dephosporylated and added with 3’adapter. The 5’ adapter was added after reverse transcription. Eventually, PCR amplification was proceeded using Phusion High-Fidelity DNA Polymerase.

value: Non-Small Cell Lung Cancer

value: RNA-Seq


title: 109_waplko_no.mcm

status: Public on Mar 07 2022

type: SRA

city: Vienna

first: Bart

middle: Johan H

last: Dequeker

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechology

library_source: genomic

data_processing:
Base calling was performed by VBCF NGS unit or MPIB NGS Core facility.
Mapping: Iterative mapping (see Imakaev et al., 2012) using bwa.
Read filtering was performed as in Flyamer et al., 2017.
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.

molecule: genomic DNA

organism: Mus musculus

source_name: zygote pronucleus

extract_protocol:
snHi-C protocol according to Flyamer et al., 2017.
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) or MPIB NGS Core facility (https://www.biochem.mpg.de/7076201/NGS) following the standard DNA sample preparation protocol.

tag: genotype

value: Waplfl/fl (Tg)Zp3-Cre

tag: strain

tag: parental origin

value: maternal

tag: cell type

value: G1 zygote


title: 16.8-year-old male with GVHD

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

country: USA

institute: Cincinnati Children's Hospital Medical Center

description:
Rectosigmoid mucosal biopsy from a 16.8-year-old male with GVHD and a diagnosis of Aplastic Anemia
SD7_S52_L008

library_source: transcriptomic

data_processing:
Following removal of primers and barcodes, reads were quantified by kallisto, with transcripts per Million (TPM) as output.
We included 14,229 protein-coding genes with TPM above 1 in 20% of samples
Genome_build: Gencode v24
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: Rectosigmoid mucosal biopsy

extract_protocol:
Rectosigmoid mucosal biopsies were obtained during lower GI endoscopy for graft-versus-host disease following hematopoietic stem cell transplant, or from controls undergoing routine clinical endoscopies unrelated to colitis or GVHD.  Samples were stored at -80C, until total RNA was extracted using the Qiagen AllPrep RNA/DNA mini kit
PolyA-RNA selection, fragmentation, cDNA synthesis, adaptor ligation and library preparation were performed using TrueSeq RNA Sample Preparation (Illumina)

tag: gvhd status

value: GVHD

tag: other dx

value: Aplastic Anemia

tag: Sex

value: male

tag: age in years

tag: tissue/sample type

value: Rectosigmoid mucosal biopsy


title: 103_waplko_no.mcm

value: paternal


title: RPMI EGFP rep 1

city: Moscow

first: Anna

last: Valyaeva

address: Leninskiye Gory, MSU, 1-73

department: Faculty of Bioengineering and Bioinformatics

country: Russia

institute: Lomonosov Moscow State University

data_processing:
Basecalling was performed using bcl2fastq v2.17.1.14.
Raw reads were aligned to GRCh38.p10 genome using HISAT2 v2.0.5 with parameters --no-softclip --dta-cufflinks; splice sites were obtained from gene annotation GENCODE v26.
Gene counts per gene were calculated using HTSeq v0.12.4 with gene annotation GENCODE v26.
Normalized counts were obtained using DESeq2 v1.30.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files with raw counts for each sample
Supplementary_files_format_and_content: Matrix table with pre-filtered and normalized gene counts for every gene and every sample

source_name: Human lymphoblastoid B cells

growth_protocol: Cells were grown at 37°C in the RPMI 1640-Gluta-Max medium (#61870-010, Gibco) with the addition of 10% embryonic serum (#SV30160.03, HyClone), sodium pyruvate (#F023 PanEco), and an antibiotic and antimycotic solution (#LS15240062, Gibco).

extract_protocol:
Cells were collected and stored in RNALater (# 76106, Quigen). Total RNA was extracted using Rneasy Mini RNA isolation kit (cat# 74134, Qiagen) following Qiagen protocol, with the following modifications: (1) lysis time is increased up to 40 min; (2) on-column DNase I treatment is performed.
cDNA libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (cat#E7760S/E7760L) by NEB following the manufacturer’s protocol. RNA was fragmented for 5 minutes.

tag: cell line

value: RPMI 8866

tag: exogenous expression

value: EGFP


title: 102_waplko_no.mcm


title: A549 input

country: China

description:
Total RNA
10mM ZnCl2
WT_In

tag: treatment


title: 9.9-year-old female with GVHD

description:
Rectosigmoid mucosal biopsy from a 9.9-year-old female with GVHD and a diagnosis of Acute Lymphoblastic Leukemia
SD4_S49_L007

value: Acute Lymphoblastic Leukemia

value: female


title: X5773660094_C_XY-_T

type: RNA

city: Los Angeles

first: Montgomery

last: Blencowe

address: 610 Charles E Young Drive East

institute: UCLA

hyb_protocol: Individual samples were hybridized to Illumina MouseRef-8 Expression BeadChips (Illumina, San Diego, CA) by Southern California Genotyping Consortium (SCGC) at UCLA

scan_protocol: Standard Illumina scanning protocol conduced by Southern California Genotyping Consortium (SCGC) at UCLA

data_processing: The data was normalized using the Lumi R package (background substraction method: 'bgAdjust'; variance stabilization method:'vst'; normalization method: 'quantile'

label: Biotin, Cy3

label_protocol: Standard illumina label protocol

growth_protocol: We used FCG mice on a C57BL/6J B6 background (B6.Cg-TgSry2Ei Srydl1Rlb/ArnoJ, Jackson Laboratories stock 10905; backcross generation greater than 20), bred at UCLA. Gonadal females and males were housed in separate cages and maintained at 23°C with a 12:12 light: dark cycle.

extract_protocol: RNA from liver and inguinal adipose tissue was isolated using Trizol (Invitrogen, Carlsbad, CA). After homogenization and centrifugation, chloroform was applied for further RNA extraction based on the protocol provided by Invitrogen.

treatment_protocol: FCG mice were gonadectomized (GDX) at 75 days of age and implanted immediately with medical grade Silastic capsules containing Silastic adhesive only (blank control, (B) or testosterone (T) or estradiol (E). Testosterone pellets contained 5mM testosterone (Steraloids, Inc., Newport, RI, USA) in a Silastic tube with 1.57mm interior diameter, 2.41mm outside diameter (Dow Corning, Midland, MI, USA). These pellets produce testosterone levels in the high physiological range. The estradiol pellets contained 50µg of 17beta-estradiol (Steraloids) dissolved in 25 µl sesame oil within a Silastic tube with interior diameter 1.98mm and 3.17mm outside diameter, sealed on the ends with 3mm of medical grade Silastic adhesive. The estradiol pellets provide sufficient estrogen to induce progestin receptors in the brain. Mice were euthanized 3 weeks later; liver and inguinal adipose tissues were dissected, snap frozen in liquid nitrogen and stored at -80°C for RNA extraction and Illumina microarray analysis. This study design produced a total of 12 groups, with 4 groups of FCG mice (XXM, XXF, XYM, XYF), where each group was further subdivided into B or T or E based on hormonal treatment: XXM_B, XXM_T, XXM_E, XYM_B, XYM_T, XYM_E, XXF_B, XXF_T, XXF_E, XYF_B, XYF_T, XYF_E.

tag: agent

value: Testosterone

value: XY-

tag: tissue

value: inguinal adipose

tag: age

value: 75 days


title: A549 sheIF4E2 rep2 input

description:
Total RNA
10mM ZnCl2
sh4E2-r2_In

value: sheIF4E2 rep2

value: Non-Small Cell Lung Cancer

value: RNA-Seq


title: HER2 WT 2

city: Houston

first: Rashi

last: Kalra

state: TX

address: ABBR R531A, One Baylor Plaza, One Baylor Plaza

department: BREAST CENTER

institute: Baylor College of Medicine

data_processing:
Alignments were performed against human genome version GRCh38 using the STAR program.
Differential expression analysis was determined through edgeR.
Gene Set Enrichment Analysis was done with the pre-ranked tool on ranked gene list. Genes were ranked based on signed p value, which was calculated as the sign of log2 fold change * -log10 (adj p value).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited txt file reports expected_count, TPM, FPKM.

molecule: polyA RNA

source_name: Lobular breast cancer cell line

growth_protocol: MM134 HER2WT and HER2L755S cells were grown in full serum media till they are 70 percent confluent. Then appropriate phenol red free media was fed to the cells supplemnted with 5 % charcoal stripped FBS for 7 days.

extract_protocol:
Cells were harvested and subjected to RNA isolation with the GE Healthcare Illustra RNA spin mini kit (Catalog # 25-0500-71)
The Genomic and RNA Profiling Core (GARP) at BCM constructed libraries with 250ng of total RNA using the TruSeq RNA Library Prep Kit (Illumina). cDNA was generated from poly(A)-selected RNA. Libraries were quantified with the KAPA Library Quantification Kit (Kapa Biosystems) and were sequenced on the NovaSeq 6000 (Illumina).

value: MM134 HER2WT

value: Lobular breast cancer cells

value: estrogen deprivation


title: 25.1-year-old female with no GVHD

description:
Rectosigmoid mucosal biopsy from a 25.1-year-old female with no GVHD and a diagnosis of Acute Lymphoblastic Leukemia
SD3_S48_L007

value: no GVHD


title: 101_waplko

value: Waplfl/fl (Tg)Zp3-Cre

value: G1 zygote


title: 100_waplko

value: maternal


title: X5773660159_H_XY-_B

value: Blank


title: RPMI Cys rep 2

value: RPMI 8866

value: TatC22G mutant protein fused with EGFP


title: X5773660104_G_XY-_B


title: A549 shM16-2 input

description:
Total RNA
10mM ZnCl2
IKD16


title: 99_waplko_no.mcm

value: paternal


title: 11.9-year-old male with no GVHD

description:
Rectosigmoid mucosal biopsy from a 11.9-year-old male with no GVHD and a diagnosis of Severe combined immunodeficiency
SD2_S47_L007

value: Severe combined immunodeficiency

value: male

value: Rectosigmoid mucosal biopsy


title: A549 sheIF4E2 rep1 input

description:
Total RNA
10mM ZnCl2
sh4E2-r1_In

value: sheIF4E2 rep1


title: HER2 WT 1


title: 7.4-year-old male with GVHD

description:
Rectosigmoid mucosal biopsy from a 7.4-year-old male with GVHD and a diagnosis of Acute Lymphoblastic Leukemia
SD1_S46_L007

value: GVHD

value: Acute Lymphoblastic Leukemia


title: X5613711015_A_XY-_B

value: XY-

value: inguinal adipose

value: 75 days


title: A549 shscramble rep2 input

description:
Total RNA
10mM ZnCl2
scr_In

value: shscramble rep2

value: Non-Small Cell Lung Cancer

value: RNA-Seq


title: 16.7-year-old male with GVHD

description:
Rectosigmoid mucosal biopsy from a 16.7-year-old male with GVHD and a diagnosis of Acute Myeloid Leukemia
PK9

value: Acute Myeloid Leukemia


title: 97_waplko_no.mcm

value: Waplfl/fl (Tg)Zp3-Cre

value: G1 zygote


title: 98_waplko_no.mcm


title: A549 shscramble rep1 input

description:
Total RNA
10mM ZnCl2
IC

value: shscramble rep1


title: 15.5-year-old male with GVHD

description:
Rectosigmoid mucosal biopsy from a 15.5-year-old male with GVHD and a diagnosis of Acute Lymphoblastic Leukemia
PK8


title: X5719882029_G_XY-_B

value: Blank


title: X5773660134_G_XXSry_E

value: Estradiol

value: XXSry


title: A549 sgM16-1 input

description:
Total RNA
10mM ZnCl2
sg16C7_In


title: A549 sgM16-2 ribo-seq

description:
Ribosome-protected RNA
Ambion™ RNase I (Thermo，AM2294)
sg16E7_Ribo

value: Ribo-Seq


title: 96_waplko_no.mcm

value: paternal


title: X5613711027_D_XY-_B


title: 27.3-year-old male with no GVHD

description:
Rectosigmoid mucosal biopsy from a 27.3-year-old male with no GVHD and a diagnosis of Dyskeratosis congenita
SD6_S51_L008

value: no GVHD

value: Dyskeratosis congenita

value: male

value: Rectosigmoid mucosal biopsy


title: 21.6-year-old female with GVHD

description:
Rectosigmoid mucosal biopsy from a 21.6-year-old female with GVHD and a diagnosis of Parox Nocturnal Hemo
PK7

value: GVHD

value: Parox Nocturnal Hemo

value: female


title: 16.9-year-old male with no GVHD

description:
Rectosigmoid mucosal biopsy from a 16.9-year-old male with no GVHD and a diagnosis of Hemophagocytic lymphohistiocytosis (XMEN)
PK6


title: X5773660159_C_XXSry_E

value: inguinal adipose

value: 75 days


title: 95_waplko_no.mcm

value: Waplfl/fl (Tg)Zp3-Cre

value: maternal


title: X5613711015_D_XXSry_E


title: 94_waplko_no.mcm

value: G1 zygote


title: A549 ribo-seq

description:
Ribosome-protected RNA
Ambion™ RNase I (Thermo，AM2294)
WT_Ribo

value: Non-Small Cell Lung Cancer


title: A549 sheIF4E2 rep2 ribo-seq

description:
Ribosome-protected RNA
Ambion™ RNase I (Thermo，AM2294)
sh4E2-r2_Ribo

value: sheIF4E2 rep2


title: 93_waplko


title: 16.6-year-old male with GVHD

description:
Rectosigmoid mucosal biopsy from a 16.6-year-old male with GVHD and a diagnosis of Acute Lymphoblastic Leukemia
PK4

value: Acute Lymphoblastic Leukemia


title: 92_waplko


title: A549 sheIF4E2 rep1 ribo-seq

description:
Ribosome-protected RNA
Ambion™ RNase I (Thermo，AM2294)
sh4E2-r1_Ribo

value: sheIF4E2 rep1

value: Ribo-Seq


title: A549 shM16-2 ribo-seq

description:
Ribosome-protected RNA
Ambion™ RNase I (Thermo，AM2294)
rKD16


title: 91_waplko_no.mcm


title: 14-year-old female with no GVHD

description:
Rectosigmoid mucosal biopsy from a 14-year-old female with no GVHD and a diagnosis of Beta Thalassemia
PK2

value: no GVHD

value: Beta Thalassemia


title: X5773660134_C_XXSry_T

value: Testosterone

value: XXSry


title: 6.7-year-old female with no GVHD

description:
Rectosigmoid mucosal biopsy from a 6.7-year-old female with no GVHD and a diagnosis of Acute Lymphoblastic Leukemia
PK3

value: Rectosigmoid mucosal biopsy


title: X5773660104_B_XXSry_T


title: 90_waplko

value: paternal


title: A549 shscramble rep2 ribo-seq

description:
Ribosome-protected RNA
Ambion™ RNase I (Thermo，AM2294)
scr_Ribo

value: shscramble rep2


title: 89_waplko


title: A549 shscramble rep1 ribo-seq

description:
Ribosome-protected RNA
Ambion™ RNase I (Thermo，AM2294)
rC

value: shscramble rep1


title: 4.7-year-old female with GVHD

description:
Rectosigmoid mucosal biopsy from a 4.7-year-old female with GVHD and a diagnosis of Aplastic Anemia
PK11

value: GVHD

value: Aplastic Anemia

value: female


title: X5613711014_E_XXSry_T

value: inguinal adipose

value: 75 days


title: X5613711027_G_XXSry_T


title: 9.4-year-old male with no GVHD

description:
Rectosigmoid mucosal biopsy from a 9.4-year-old male with no GVHD and a diagnosis of Acute Myeloid Leukemia
PK10

value: Acute Myeloid Leukemia

value: male


title: 88_waplko

value: Waplfl/fl (Tg)Zp3-Cre

value: G1 zygote


title: 12.5-year-old male with no GVHD

description:
Rectosigmoid mucosal biopsy from a 12.5-year-old male with no GVHD and a diagnosis of CD40 Ligand Deficiency
PK1

value: no GVHD

value: CD40 Ligand Deficiency


title: X5773660094_B_XXSry_T

value: Testosterone


title: X5773660159_G_XXSry_B

value: Blank

value: XXSry


title: PBMC-02-2-GEX-S2

city: San Francisco

first: Wilson

last: Liao

state: CA

address: 2340 Sutter St.

department: Dermatology

institute: University of California, San Francisco

description:
PBMC-02-2.barcodes.tsv.gz
PBMC-02-2.features.tsv.gz
PBMC-02-2.matrix.mtx.gz

data_processing:
Library strategy: CITE-seq
Raw RNA and ADT fastqs for each Chromium library were respectively aligned to the GRCh38 human genome reference and a reference database of antibody-tag sequences using Cell Ranger 3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: CellMetadata_AS_20220103.tsv, CellMetadata_PSA_20220103.tsv: metadata for each barcode (cell type, subject, subject clinical status, whether the cell was identified to be a doublet, etc.); barcodes.tsv.gz: cell barcodes in the sample; features.tsv.gz: Gene and ADT features detected in a sample; matrix.mtx.gz: MTX (MatrixMarket)-formatted read counts in a sample of each feature in the corresponding features.tsv.gz file in each barcode in the corresponding barcodes.tsv.gz file

source_name: peripheral blood mononuclear cells

extract_protocol:
A pooled suspension containing 2,000,000 thawed PBMCs from at most 20 subjects (~100,000 per subject) were stained with 282 Totalseq antibodies according to the Totalseq-A protocol (https://www.biolegend.com/en-us/protocols/totalseq-a-antibodies-and-cell-hashing-with-10x-single-cell-3-reagent-kit-v3-3-1-protocol). Stained cells were then loaded onto the Chromium Controller at an input density of 2,500 cells/µL and cDNA libraries were prepared using the 10X Genomics Single Cell 3' v3.1 Assay.
Peripheral blood was collected from each subject in Vacutainer ACD tubes. PBMCs were isolated using a standard Ficoll method and stored in liquid nitrogen.

tag: batchid

tag: subbatchid

tag: sequencingrunid

tag: librarytype

value: Gene Expression


title: PBMC-02-3-ADT-S2

description:
PBMC-02-3.barcodes.tsv.gz
PBMC-02-3.features.tsv.gz
PBMC-02-3.matrix.mtx.gz

extract_protocol:
Libraries of antibody-derived tags (ADT) from feature barcoding antibodies were prepared by repeating size purification on the supernatant obtained from the prior size purification of gene expression cDNA libraries (Step 2.3.d in the manufacturer’s instructions https://assets.ctfassets.net/an68im79xiti/1eX2FPdpeCgnCJtw4fj9Hx/7cb84edaa9eca04b607f9193162994de/CG000204_ChromiumNextGEMSingleCell3_v3.1_Rev_D.pdf), using a 7:8 volumetric ratio of 2.0X SPRIselect reagent (Beckman Coulter, Cat# B23317) to sample. Indexing amplification was performed using Kapa Hifi HotStart ReadyMix (Kapa Biosystems, Cat# KK2601) and TruSeq Small RNA RPI primers (Illumina) with the following thermocycling conditions: (1) 98 °C, 2 min; (2) 15 × (98 °C, 20 sec; 60 °C, 30 sec; 72 °C, 20 sec); (3) 72 °C, 5 min. Size purification was then repeated on amplified libraries using a 5:6 volumetric ratio of 1.2X SPRIselect reagent to sample.
Peripheral blood was collected from each subject in Vacutainer ACD tubes. PBMCs were isolated using a standard Ficoll method and stored in liquid nitrogen.

value: Antibody Capture


title: 87_waplko

tag: genotype

tag: strain

tag: parental origin

value: paternal


title: 86_waplko_no.mcm

value: maternal

tag: cell type


title: A549 sgM16-1 ribo-seq

description:
Ribosome-protected RNA
Ambion™ RNase I (Thermo，AM2294)
sg16C7_Ribo

value: Non-Small Cell Lung Cancer

value: Ribo-Seq


title: AUX_TRP_3

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
library strategy: micro-C
Base calling was performed by VBCF NGS unit or MPIB NGS Core facility
Data were processed using distiller-nf pipeline using this project.yml file: https://gist.github.com/Phlya/3dc64b6152bbcd9d7a2f52ccf22ad35f
Genome_build: hg38
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 2kb, 5kb,10kb, 25kb, 50kb, 100kb, 250kb, 500kb and 1Mb resolutions stored in the mcool file format. For micro-C data, additionally 100, 200, 500 bp resolutions are included. Also, pair files describing detected deduplicated interacting pairs.

source_name: HCT116 MCM2-AID

growth_protocol: HCT116 cells were cultured as previously described (9). Briefly, cells were cultured in McCoy’s 5A medium (Thermo Fisher Scientific) supplemented with 10% FBS (Gibco), 2 mM L-glutamine (Invitrogen) and 10% penicillin-streptomycin solution (Sigma-Aldrich). Cells were grown in an incubator at 37˚C with 5% CO2.

extract_protocol:
Hi-C was performed largely as described in Rao et al, 2014 with minor modifications. Briefly, ~5x10 6 HCT116 cells were crosslinked in 1% formaldehyde for 10 min at RT, snap-frozen and stored at -80°C. After permeabilization in lysis buffer (0.2% Igepal, 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 1x Halt Protease inhibitor cocktail) nuclei were isolated in 0.3% SDS in NEBuffer 3 at 62°C for 10 min. SDS was quenched with 1% Triton X-100 at 37°C for 1 h, then the nuclei were pelleted and resuspended in 250 μl DpnII buffer with 600 U DpnII (New England Biolabs) at 37˚C. After overnight digestion, 200 U DpnII were added for 2 h more incubation. Then, the ends were filled-in with d(G/C/T)TPs and biotin-14-dATP (Life Technologies) using Klenow (New England Biolabs) for 1.5 h at 37°C. After ligation at room temperature for 4 h with T4 ligase (New England Biolabs), the nuclei were spun down, resuspended in 200 μl mQ and digested with proteinase K for 30 min at 55°C in presence of 1% SDS. Cross-links were reversed at 65°C overnight after addition of NaCl to a final concentration of 1.85 M. After ethanol precipitation and a 70%–80% ethanol wash, DNA was resuspended in 50 µl of 10 mM Tris EDTA, incubated on ice for 15 min and then sheared to ~300-1300 bp fragments using the E220 Focused-ultrasonicator (Covaris). DNA was bound to MyOne C1 Streptavidin beads (ThermoFischer) and used for library preparation with the NEB Next Ultra Library Prep kit (Illumina). Micro-C was performed using the Dovetail micro-C kit. Libraries were sequenced on the NovaSeq 6000 system with 100 bp paired-end reads (at VBCF NGS Unit)
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) or MPIB NGS Core facility (https://www.biochem.mpg.de/7076201/NGS) following the standard DNA sample preparation protocol.

treatment_protocol: MCM2-mAID degradation was induced by addition of 500 µM 3-indoleacetic acid (Sigma-Aldrich) for 7 h. To synchronize cells in G1, a 2 mM thymidine arrest was followed by release into fresh medium for 6 h. Subsequently, nocodazole was added for 5 h, followed by shake-off of prometaphase cells and release in fresh medium for 5 h.

value: Auxin and triptolide (TRP)

tag: molecule type

value: Proximity ligated gDNA


title: PBMC-02-3-GEX-S2


title: 7.8-year-old female with GVHD

description:
Rectosigmoid mucosal biopsy from a 7.8-year-old female with GVHD and a diagnosis of Acute Lymphoblastic Leukemia
PK5

tag: gvhd status

value: GVHD

tag: other dx

value: Acute Lymphoblastic Leukemia

tag: Sex

value: female

tag: age in years

value: Rectosigmoid mucosal biopsy


title: X5773660104_F_XY-Sry_B

value: XY-Sry

value: inguinal adipose

value: 75 days


title: PBMC-02-4-ADT-S2

description:
PBMC-02-4.barcodes.tsv.gz
PBMC-02-4.features.tsv.gz
PBMC-02-4.matrix.mtx.gz


title: AUX_TRP_2

tag: treatment


title: 85_waplko_no.mcm

value: Waplfl/fl (Tg)Zp3-Cre

value: G1 zygote


title: AUX_TRP_1


title: PBMC-02-4-GEX-S2

value: Gene Expression


title: X5613711015_H_XXSry_B

tag: agent

value: Blank

value: XXSry


title: X5773660094_F_XXSry_E

value: Estradiol

tag: tissue


title: X5613711027_C_XXSry_B

tag: age


title: 84_waplko_no.mcm

value: maternal


title: PBMC-02-1-ADT-S2

description:
PBMC-02-1.barcodes.tsv.gz
PBMC-02-1.features.tsv.gz
PBMC-02-1.matrix.mtx.gz

tag: batchid

value: Antibody Capture


title: DMSO_TRP_2

value: DMSO and triptolide (TRP)


title: DMSO_TRP_3

value: Proximity ligated gDNA


title: 83_waplko_no.mcm


title: X5719882029_F_XXSry_B


title: 82_waplko_no.mcm

value: paternal


title: PBMC-02-1-GEX-S2

tag: subbatchid


title: X5773660159_B_XY-Sry_E


title: X5773660134_F_XY-Sry_E


title: DMSO_TRP_1


title: G1_AUX_r2_3

value: Auxin


title: PBMC-03-3-ADT-S3

description:
PBMC-03-3.barcodes.tsv.gz
PBMC-03-3.features.tsv.gz
PBMC-03-3.matrix.mtx.gz

tag: sequencingrunid


title: 81_waplko_no.mcm


title: 80_waplfl

value: Waplfl/fl


title: PBMC-03-3-GEX-S3

tag: librarytype


title: X5613711014_H_XY-Sry_E

tag: genotype


title: G1_AUX_r2_2


title: PBMC-03-2-ADT-S3

description:
PBMC-03-2.barcodes.tsv.gz
PBMC-03-2.features.tsv.gz
PBMC-03-2.matrix.mtx.gz


title: 79_waplfl

tag: strain


title: G1_AUX_r2_1


title: PBMC-03-2-GEX-S3


title: 78_waplfl

tag: parental origin


title: X5773660094_E_XY-Sry_E


title: G1_DMSO_r2_3

value: DMSO


title: G1_DMSO_r2_2


title: PBMC-03-1-ADT-S3

description:
PBMC-03-1.barcodes.tsv.gz
PBMC-03-1.features.tsv.gz
PBMC-03-1.matrix.mtx.gz


title: X5773660134_B_XY-Sry_T

value: Testosterone

value: XY-Sry


title: PBMC-03-1-GEX-S3


title: G1_DMSO_r2_1


title: 77_waplfl

tag: cell type


title: 76_waplfl


title: X5773660104_A_XY-Sry_T

value: inguinal adipose

value: 75 days


title: 75_waplko

value: Waplfl/fl (Tg)Zp3-Cre

value: G1 zygote


title: G1_AUX_4

tag: molecule type


title: 74_waplko


title: X5613711014_D_XY-Sry_T


title: X5613711027_F_XY-Sry_T


title: PBMC-03-4-GEX-S3

description:
PBMC-03-4.barcodes.tsv.gz
PBMC-03-4.features.tsv.gz
PBMC-03-4.matrix.mtx.gz

value: Gene Expression


title: G1_AUX_3


title: X5773660094_A_XY-Sry_T


title: 73_waplko


title: PBMC-05-3-GEX-S5

description:
PBMC-05-3.barcodes.tsv.gz
PBMC-05-3.features.tsv.gz
PBMC-05-3.matrix.mtx.gz


title: 72_waplko


title: PBMC-05-3-ADT-S5


title: G1_AUX_2


title: PBMC-05-1-ADT-S5

description:
PBMC-05-1.barcodes.tsv.gz
PBMC-05-1.features.tsv.gz
PBMC-05-1.matrix.mtx.gz


title: G1_AUX_1


title: X5613711015_C_XY-Sry_E


title: 71_waplko


title: PBMC-05-1-GEX-S5


title: X5773660104_E_XY-Sry_B

value: Blank


title: 69_waplko


title: G1_DMSO_3


title: G1_DMSO_4


title: PBMC-05-2-ADT-S5

description:
PBMC-05-2.barcodes.tsv.gz
PBMC-05-2.features.tsv.gz
PBMC-05-2.matrix.mtx.gz


title: G1_DMSO_2


title: 70_waplfl


title: G1_DMSO_1


title: PBMC-03-4-ADT-S3


title: X5613711027_B_XXSry_B

value: XXSry


title: X5613711015_G_XY-Sry_B


title: 68_waplko


title: 66_waplko

value: maternal


title: 67_waplfl


title: PBMC-05-2-GEX-S5


title: 5719882028_A_XX_E

value: Estradiol

value: XX

value: liver


title: DMSO2.RNAseq.HCT116MCM2mAID

data_processing:
FastQ files were pseudoaligned using Kallisto with 100 bootstraps (Bray et al., 2016). To find differentially expressed transcripts we used Wald test for Sleuth model (sleuth) in R. GO term enrichment of molecular functions of up- and downregulated genes were carried out using ShinyGO (http://bioinformatics.sdstate.edu/go/).
Genome_build: hg38
Supplementary_files_format_and_content: The processed abundance.h5 files are HDF5 binary files containing run info, abundance estimates, bootstrap estimates, and transcript length information length. These files can be read in by sleuth, a companion package for Kallisto which is used for differential expression analysis of transcript quantifications from Kallisto (Harold et al., 2017).

source_name: HCT116 cells

growth_protocol: Cells were cultured in McCoy’s 5A medium (Thermo Fisher Scientific) supplemented with 10% FBS (Gibco), 2 mM L-glutamine (Invitrogen) and 10% penicillin-streptomycin solution (Sigma-Aldrich).

extract_protocol:
Total RNA from HCT116 cells were isolated using a lysis step based on guanidine thiocyanate (adapted from (Boom et al., 1990) and using magnetic beads (GE Healthcare, 65152105050450). mRNA sequencing libraries were prepared from 1 µg total RNA.
mRNA sequencing libraries were prepared from 1 µg total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760). Paired-end sequencing was performed on Illumina NextSeq 500 (2 x 43 bp reads). Total 6 samples were multiplexed and sequenced on a NextSeq 500/550 High Output Kit v2.5 (75 Cycles) at MPIB NGS Core facility (www.biochem.mpg.de/7076201/NGS). BCL raw data were converted to FASTQ data and demultiplexed by bcl2fastq.
mRNA-Seq

treatment_protocol: MCM2-mAID degradation was induced by addition of 500 µM 3-indoleacetic acid (Sigma-Aldrich).

tag: cell line

value: HCT116 cells

value: HCT116 MCM2-mAID cells

value: dmso


title: X5773660159_F_XY-Sry_B


title: 5719882029_D_XX_E


title: PBMC-05-4-GEX-S5

description:
PBMC-05-4.barcodes.tsv.gz
PBMC-05-4.features.tsv.gz
PBMC-05-4.matrix.mtx.gz


title: 5719882002_H_XX_E


title: DMSO1.RNAseq.HCT116MCM2mAID


title: PBMC-04-3-ADT-S4

description:
PBMC-04-3.barcodes.tsv.gz
PBMC-04-3.features.tsv.gz
PBMC-04-3.matrix.mtx.gz

value: Antibody Capture


title: PBMC-04-3-GEX-S4


title: 5719882006_B_XX_E


title: 64_waplko

value: paternal


title: 5613703020_E_XX_E


title: AUX2.RNAseq.HCT116MCM2mAID

value: auxin


title: AUX3.RNAseq.HCT116MCM2mAID


title: PBMC-04-4-ADT-S4

description:
PBMC-04-4.barcodes.tsv.gz
PBMC-04-4.features.tsv.gz
PBMC-04-4.matrix.mtx.gz


title: PBMC-05-4-ADT-S5


title: 62_waplko


title: AUX1.RNAseq.HCT116MCM2mAID


title: PBMC-04-4-GEX-S4


title: DMSO3.RNAseq.HCT116MCM2mAID


title: 5719882028_E_XX_T

value: Testosterone


title: 61_waplfl

value: Waplfl/fl


title: 60_b6129svcba_no.mcm

value: wild type


title: PBMC-04-2-ADT-S4

description:
PBMC-04-2.barcodes.tsv.gz
PBMC-04-2.features.tsv.gz
PBMC-04-2.matrix.mtx.gz


title: 65_waplko

value: Waplfl/fl (Tg)Zp3-Cre

value: G1 zygote


title: PBMC-04-2-GEX-S4

value: Gene Expression


title: 5719882013_C_XX_T

value: 75 days


title: 11: TM4_Sertoli_Control

city: St-Hyacinthe

first: Younes

last: Chorfi

state: Québec

address: 3200 Sicotte

country: Canada

institute: Université de Montreal

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode M23
Expression values were also computed using RSEM version 1.2.28 based on Gencode version M23 transcript annotations
Genome_build: GRCh38
Supplementary_files_format_and_content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary_files_format_and_content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

source_name: TM4 Sertoli  (ATCC CRL-1715)

growth_protocol: TM4 mouse Sertoli cell line was cultured at 37℃ in a 5% CO2 incubator with DMEM/F12 medium (Life technologies, Burlington, ON, Canada) supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin, 0.25 µg/ml fungizone (Life technologies), 15 mM HEPES, 5% horse serum and 2.5 % fetal bovine serum at 37°C for 24 h in a humidified 5% CO2 incubatorTM4 cells were prepared in 6-well plates to a concentration of 2.5 × 10E5 viable cells.

extract_protocol:
RNeasy mini kit (Qiagen)
Kapa RNA HyperPrep (Roche) using a poly-A selection (Thermo Scientific)

treatment_protocol: After 24h of incubation, cells were exposed to Zearalenone (20 µM) or vehicle (ethanol) for 24h

tag: tissues

value: testis

value: TM4 Sertoli

value: Ethanol


title: PBMC-04-1-ADT-S4

description:
PBMC-04-1.barcodes.tsv.gz
PBMC-04-1.features.tsv.gz
PBMC-04-1.matrix.mtx.gz


title: 59_b6129svcba_no.mcm

value: maternal


title: 12: TM4_Sertoli_Control


title: 10: TM4_Sertoli_Control


title: 5719882030_B_XX_T

value: XX

value: liver


title: 58_b6129svcba_no.mcm


title: 5719882006_F_XX_T


title: 63_waplko


title: PBMC-06-4-GEX-S7

description:
PBMC-06-4.barcodes.tsv.gz
PBMC-06-4.features.tsv.gz
PBMC-06-4.matrix.mtx.gz


title: 5719882030_F_XX_B

value: Blank


title: PBMC-04-1-GEX-S4


title: 57_b6129svcba_no.mcm


title: 5613703028_H_XX_T


title: 8: TM4_Sertoli_Zearalenone

value: Zearalenone (20uM)


title: 56_b6129svcba_wt.ctrl

value: paternal


title: 5719882013_G_XX_B


title: PBMC-06-4-ADT-S6

value: Antibody Capture


title: 7: TM4_Sertoli_Zearalenone


title: 55_b6129svcba_wt.ctrl


title: PBMC-06-2-GEX-S7

description:
PBMC-06-2.barcodes.tsv.gz
PBMC-06-2.features.tsv.gz
PBMC-06-2.matrix.mtx.gz


title: 6: TM4_Sertoli_Control


title: 5613703020_A_XX_B


title: 54_b6129svcba_no.mcm


title: 53_b6129svcba_no.mcm


title: PBMC-06-3-GEX-S7

description:
PBMC-06-3.barcodes.tsv.gz
PBMC-06-3.features.tsv.gz
PBMC-06-3.matrix.mtx.gz


title: 2: TM4_Sertoli_Zearalenone


title: PBMC-06-2-ADT-S6


title: 5: TM4_Sertoli_Control


title: 51_b6129svcba_no.mcm


title: PBMC-06-3-ADT-S6


title: 52_b6129svcba_no.mcm


title: 50_b6129svcba_wt.ctrl


title: 4: TM4_Sertoli_Control


title: 3: TM4_Sertoli_Zearalenone


title: 5719882002_G_XY-_E

value: Estradiol

value: XY-


title: 5613703028_D_XX_B


title: 9: TM4_Sertoli_Zearalenone


title: 5719882002_D_XX_B


title: 49_b6129svcba_wt.ctrl

value: wild type


title: 5719882028_H_XY-_E


title: 5719882029_A_XY-_E


title: PBMC-06-1-GEX-S7

description:
PBMC-06-1.barcodes.tsv.gz
PBMC-06-1.features.tsv.gz
PBMC-06-1.matrix.mtx.gz


title: 5719882006_A_XY-_E


title: 1: TM4_Sertoli_Zearalenone


title: PBMC-07-3-ADT-S8

description:
PBMC-07-3.barcodes.tsv.gz
PBMC-07-3.features.tsv.gz
PBMC-07-3.matrix.mtx.gz


title: 5719882028_D_XY-_T

value: Testosterone


title: 46_b6129svcba_wt.ctrl

value: G1 zygote


title: 57-PanxKOEPINap200D4

city: Charlottesville

first: Eugene

last: Ke

state: Virginia

address: P.O. Box 800734, 1340 Jefferson Park Avenue

department: MIC

institute: University of Virginia

data_processing:
Reads were checked for quality using FASTQC (v0.11.8)
Trimmed using BBMAP (v3.8.16b)
Aligned to the mouse genome with GENCODE (vM22) annotations using STAR (v2.7.1a) using ENCODE parameters
Transcripts per million calculations were performed by RSEM (v1.3.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text files for each sample of the gene-level abundance estimates as generated by RSEM

source_name: purified lung epithelium

growth_protocol: After induction of napthalene induced injury, lung epithelium was purifed by cell sorted

extract_protocol:
RNA was isolated by Nucelospin RNA isolation kit with on-column DNASE digestion (Machery-Nagel)
mRNA libraries were perpared using the Truseq Stranded mRNA kit following the manufacturer's protocol (Illumina); Paired-End, 75 base-pairs

treatment_protocol: Napthalene was dissolved in sterie corn oil and administered as a single i.p. injection at a dose of either 160mg/kg or 200mg/kg

value: lung

value: epithelium

tag: Sex

value: female

value: 8-14 weeks

tag: cell markers

value: CD45-/CD31-/EpCAM+ live singlets

value: 200mg/kg Napthalene


title: 60-PanxKOEPINap200D4

tag: treatment


title: 58-PanxKOEPINap200D4


title: 59-PanxKOEPINap200D4


title: 45_b6129svcba_wt.ctrl


title: PBMC-07-3-ADT-S6


title: 5719882030_A_XY-_T

tag: agent

value: 75 days


title: 55-WTEPINap200D4

tag: tissue


title: 48_b6129svcba_wt.ctrl

value: maternal


title: 43_b6129svcba_no.mcm


title: PBMC-01-4-GEX-S1

description:
PBMC-01-4.barcodes.tsv.gz
PBMC-01-4.features.tsv.gz
PBMC-01-4.matrix.mtx.gz

value: Gene Expression


title: 56-PanxKOEPINap200D4

tag: age


title: 5719882013_B_XY-_T

value: liver


title: 42_b6129svcba_wt.ctrl

value: paternal


title: 44_b6129svcba_no.mcm


title: PBMC-01-2-GEX-S1

description:
PBMC-01-2.barcodes.tsv.gz
PBMC-01-2.features.tsv.gz
PBMC-01-2.matrix.mtx.gz

tag: batchid


title: 5613703020_D_XY-_E


title: PBMC-07-4-GEX-S7

description:
PBMC-07-4.barcodes.tsv.gz
PBMC-07-4.features.tsv.gz
PBMC-07-4.matrix.mtx.gz

tag: subbatchid


title: PBMC-07-3-GEX-S7

tag: sequencingrunid


title: 54-WTEPINap200D4


title: 47_b6129svcba_wt.ctrl


title: 5719882030_E_XY-_B

value: Blank


title: 5613703028_G_XY-_T


title: PBMC-07-2-GEX-S7

description:
PBMC-07-2.barcodes.tsv.gz
PBMC-07-2.features.tsv.gz
PBMC-07-2.matrix.mtx.gz

tag: librarytype


title: 5719882006_E_XY-_T

tag: genotype


title: 41_b6129svcba_wt.ctrl

tag: strain


title: 53-WTEPINap200D4


title: 5719882002_C_XY-_B


title: 52-WTEPINap200D4


title: PBMC-07-1-GEX-S7

description:
PBMC-07-1.barcodes.tsv.gz
PBMC-07-1.features.tsv.gz
PBMC-07-1.matrix.mtx.gz


title: PBMC-01-1-GEX-S1

description:
PBMC-01-1.barcodes.tsv.gz
PBMC-01-1.features.tsv.gz
PBMC-01-1.matrix.mtx.gz


title: 5719882013_F_XY-_B


title: PBMC-01-3-GEX-S1

description:
PBMC-01-3.barcodes.tsv.gz
PBMC-01-3.features.tsv.gz
PBMC-01-3.matrix.mtx.gz


title: 5613703020_H_XY-_B


title: 5613703028_C_XY-_B


title: 40_b6129svcba_wt.ctrl

tag: parental origin


title: 51-WTEPINap200D4

tag: cell type


title: Distal alveolar cells- Control

city: Bangalore

first: Rajarshi

last: Pal

address: CCAMP, NCBS

country: India

institute: Eyestem research

data_processing:
Adapter Trimming was performed using Trimmomatic (v-0.36)
Contamination removal was performed using Bowtie2 (2.2.4).The unwanted sequences like - mitochondrial genome sequences, ribosomal RNAs, transfer RNAs are removed in this step.
The paired-end reads are aligned to the reference human genome (hg19). Alignment was performed using HISAT2 (2.1.0).
The aligned reads are used for estimating expression of the genes. The raw read counts were estimated using FeatureCount (1.5.2). Read count data were normalized using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include rawcounts for each Sample

source_name: Induced pluripotent stem cells

growth_protocol: Specific combinatorial cocktail used to generate lung epithelial cells from induced pluripotent stem cells.

extract_protocol:
Lung epithelial cells were generated from induced pluripotent stem cells and infected with SARS-CoV-2 virus at different MOI and different time points. RNA was isolated and sequenced from the control uninfected and SARS-CoV-2 infected cells.
RNA libraries were prepared for sequencing using NEB Ultra II directional RNA-Seq Library Prep kit (NEB, Cat# E7760L), with rRNA depletion using RiboCop rRNA Depletion Kit from Lexogen

treatment_protocol: Lung epithelial cell types infected at 5MOI (multiplicities of infection) and harvested at 2 different timepoints

value: Distal alveolar cells

tag: infection

value: control

tag: time


title: Proximal airway cells- 24 hours post infection

value: Proximal airway cells

value: SARS-CoV-2 virus

value: 24 hours post infection


title: 39_b6129svcba_wt.ctrl

value: wild type

value: G1 zygote


title: Distal alveolar cells- 24 hours post infection


title: Distal alveolar cells- 72 hours post infection

value: 72 hours post infection


title: Proximal airway cells- 72 hours post infection


title: 38_b6129svcba_wt.ctrl


title: 5719882028_G_XXSry_E

value: Estradiol

value: XXSry


title: 36_b6129svcba_wt.ctrl


title: 37_b6129svcba_wt.ctrl


title: 5719882006_H_XXSry_E


title: 5719882029_B_XXSry_E


title: 34_b6129svcba_wt.ctrl


title: 35_b6129svcba_wt.ctrl


title: Proximal airway cells- Control


title: Lung Progenitors- 24 hours post infection

value: Lung Progenitors


title: 5719882002_F_XXSry_E

value: 75 days


title: 33_b6129svcba_wt.ctrl


title: 5613703020_C_XXSry_E


title: Lung Progenitors- 72 hours post infection


title: Lung Progenitors- Control


title: 5719882013_A_XXSry_T

value: Testosterone


title: 32_b6129svcba_wt.ctrl

value: maternal


title: MKL-1 EPZ011989 H3K4me3 - Rep 2

city: Boston

first: Ashley

middle: K.

last: Gartin

state: MA

address: 450 Brookline Ave. Mayer 444

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Library strategy: CUT&RUN
Illumina basecalling was performed by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.
Read quality was checked by FastQC.
Files were aligned separately to hg38 and E. coli K-12 GCA_004919995 using bowtie 2 version 2.2.9 with commands --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Samtools version 0.1.19 view was used to downsample the aligned human reads according to the number of aligned E. coli reads per sample. Bam files were converted to .bw
Macs2 version 2.1.1.20160309 was used to call peaks with the following options: For H3K4me3 and IgG narrowPeak files were generated: -q 0.05 -f BAMPE --keep-dup all --nolambda; For H3K27me3 broadPeak files were generated: -q 0.05 -f BAMPE --keep-dup all --nolambda --broad --broad-cutoff 0.1
Genome_build: hg38 and E. coli K-12 GCA_004919995
Supplementary_files_format_and_content: .bw files contain downsampled aligned read pileups for each sample; .narrowPeak and .broadPeak files contain genome coordinates, scores, and p-values called by macs2 for each sample.

source_name: MKL-1 Merkel cell carcinoma cell line

growth_protocol: MKL-1 cells were maintained in RPMI medium with 10% FBS at 37 °C and 5% CO2.

extract_protocol:
Cells were treated with Accutase and samples were split into thirds, bound to ConA beads, and permeabilized with 0.025% digitonin. Antibodies were added for overnight incubation at 4 °C. After 30 min incubation with pA-Mnase plus calcium, stop buffer containing RNase A and 200 pg/mL E. coli spike-in DNA was added. DNA was extracted using a standard phenol/chloroform protocol.
Libraries were constructed using automated Swift 2S ligation chemistry.

treatment_protocol: 36E4 cells were plated at 12E4 cells/mL with 1% ethanol or 3 µM EPZ011989 in a final concentration of 1% ethanol. Cells were split approximately 1:2 into larger dishes with complete media refreshment on day 3 and harvested on day 6.

value: 3 µM EPZ011989 in 1% ethanol

tag: cut&run antibody

value: 1:100 rabbit anti-H3K4me3 (Active Motif 39060)

tag: cell line


title: 31_b6129svcba_wt.ctrl

value: paternal


title: STING-polysome-seq_2

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
Polysome-Seq was performed with biological replicates for all samples. Raw reads were trimmed to 50 bp and mapped to the human genome (hg19) using Tophat v2.1.1 with default parameters. Only uniquely mapped reads were subsequently assembled into transcripts guided by the reference annotation (UCSC gene models) using Cufflinks v2.2.1. The RNA abundance of each gene was quantified with FPKM (fragments per kilobase of exon per million mapped fragments).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values of all Polysome-seq samples

source_name: HEK293 cells

growth_protocol: HEK293 cells were obtained from ATCC, and  were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) at 37°C in 5% CO2 (v/v).

extract_protocol:
Cells transfected with different plasmids  were pretreated with 100 mg/ml cycloheximide for 30 min at 37°C prior to washing with ice-cold PBS containing 100 mg/ml cycloheximide. Cells were then lysed in polysome lysis buffer (20 mM Tris-HCl (pH 7.4), 100 mM KCl, 5 mM MgCl2, 100 mg/ml cycloheximide and 1% NP40). After 20 min on ice, the lysates were centrifuged (12,000 rpm for 15 min at 4°C), and the supernatants were loaded onto 10-50% sucrose gradients and centrifuged for 15 h at 25,000 rpm and 4°C in a SW41 rotor. Separated samples were fractionated at 0.75 ml/min through an automated fractionation system that continually monitors OD254 values. An aliquot of the ribosomal fraction was used for extraction of total RNA with TRIzol reagent (Yeasen). Purified RNAs were used for cDNA synthesis using the Smart-seq2 method (Picelli et al., 2014). Briefly, the polyadenylated mRNAs were captured usingby the PolyT primers. After 3 min lysis at 72°C, the Smart-seq2 reverse transcription reactions were performed. After the first-strand reaction, the cDNA was amplified using a limited number of cycles (12∼14 cycles).
Sequencing libraries were constructed from 1 ng of amplified cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) according to the manufacturer's instructions. Barcoded libraries were pooled and sequenced on the Illumina HiSeq X Ten platform in the 150 bp paired-end mode.

treatment_protocol: A total of 7x10^6 cells were transfected with 5ug Vector or STING plasmid for 24 hours.

value: Ectopic expression of STING

tag: fraction

value: Polysome


title: 5719882030_H_XXSry_T

value: liver


title: 30_b6129svcba_wt.ctrl


title: 5719882006_D_XXSry_T


title: MKL-1 EPZ011989 H3K4me3 - Rep 1

tag: treatment


title: STING-polysome-seq_1


title: 5719882028_C_XXSry_T

tag: agent


title: 5613703028_F_XXSry_T

tag: tissue


title: MKL-1 EPZ011989 H3K27me3 - Rep 2

value: 1:100 rabbit anti-Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technologies 9733)


title: Vector-polysome-seq_2

value: Ectopic expression of Vector


title: 27_b6129svcba_no.mcm

value: wild type


title: 28_b6129svcba_wt.ctrl

value: G1 zygote


title: Eca109_after Interference_replicate 3 [siRNA-3]

city: Shijiazhuang

last: Jing

state: Hebei

address: NO12 Jiankang Road

department: Department of Medical Oncology

institute: the Fourth Hospital of Hebei Medical University

data_processing:
Basecalls was performed using CASAVA version 1.4
During data pre-processing, Seqtk was applied to remove adaptor sequences, bases with quality value lower than 20 at 3'-end, reads shorter than 25bp, and ribosome RNA reads.
Reads were mapped to hg38 genome assembly with the spliced mapping algorithm of Hisat2 (version 2.0.4).
Gene expression was quantified and then normalized as FPKM(Fragments Per Kilobase of exon model per Million mapped reads). In this step, fragments of each gene were counted and normalized into trimmed mean of M values (TMM), after which FPKM values of every gene were calculated by Perl scripts.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM and counts

source_name: Eca109 transfected with LSINCT5 siRNA

growth_protocol: Eca109 were cultured in RPMI-1640 medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, Gaithersburg, MD,USA) and maintained in a humidified incubator at 37°C with 5% CO2

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 integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eca109 were seeded in 6-well plates for 24 h and then transfected with designed siRNA (100 nmol/L)  with Lipofectamine RNAi MAX (Invitrogen) in serum-free medium, according to the manufacturer’s protocols. After transfection, cells were harvested for subsequent analyses

value: esophageal squamous cell carcinoma cell line

tag: genotype/variation

value: LSINCT5 knockdown


title: MKL-1 EPZ011989 IgG - Rep 2

value: 1:100 rabbit anti-mouse IgG (Abcam ab46540)


title: 5719882030_D_XXSry_B

value: Blank

value: XXSry

tag: age


title: 26_b6129svcba_no.mcm


title: 5719882002_B_XXSry_B

value: 75 days


title: 5613703020_G_XY-Sry_B

value: XY-Sry


title: MKL-1 EPZ011989 IgG - Rep 1

value: 3 µM EPZ011989 in 1% ethanol


title: Eca109_after Interference_replicate 2 [siRNA-2]


title: 25_b6129svcba_no.mcm

value: maternal


title: Eca109_after Interference_replicate 1 [siRNA-1]


title: MKL-1 Vehicle H3K4me3 - Rep 2

value: 1% ethanol

value: 1:100 rabbit anti-H3K4me3 (Active Motif 39060)


title: Eca109_before Interference_replicate 3 [NC-3]

value: control


title: 24_b6129svcba_no.mcm

value: paternal


title: MKL-1 Vehicle H3K4me3 - Rep 1


title: 5719882013_E_XXSry_B

value: liver


title: 29_b6129svcba_wt.ctrl


title: MKL-1 Vehicle H3K27me3 - Rep 2

value: 1:100 rabbit anti-Tri-Methyl-Histone H3 (Lys27) (Cell Signaling Technologies 9733)


title: Eca109_before Interference_replicate 2 [NC-2]


title: 23_b6129svcba_no.mcm

value: wild type


title: Vector-polysome-seq_1

value: Ectopic expression of Vector

value: Polysome


title: 5719882028_F_XY-Sry_E

value: Estradiol


title: MKL-1 EPZ011989 H3K27me3 - Rep 1


title: MKL-1 Vehicle H3K27me3 - Rep 1


title: 21_b6129svcba_no.mcm

value: G1 zygote


title: Neg-Ctrl-2

city: Taipei

first: Bon-chu

last: Chung

state: Taiwan

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: SMART-seq HT Kit

data_processing:
Sequencing was performed on an Illumina NextSeq500  platform in a 75-base paired-end mode.Illumina NextSeq Control software and RTA  used for basecalling.
sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a
expected count, TPM and FPKM were calculated by RSEM v1.3.1
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene id, transcript id, expected count, TPM and FPKM for each sample

organism: Danio rerio

source_name: trunk cell

extract_protocol:
Gonads were dissected, Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART-seq HT Kit (Takara, Cat. 634438). The SMART-seq HT Kit was then used for reverse transcription and cDNA amplification.  In SMART-seq HT, full-length cDNA was synthesized in one step, and then amplified by 12 cycles of PCR. After purification with the AMPure XP kit (Beckman Coulter), cDNAs were analyzed by a bioanalyzer for their qualities.
cDNA libraries were generated using the SMART-seq HT Kit (Takara, Cat. 634438). Final libraries were prepared using Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096).

value: Nadia/Tupfel long-fin hybrid

value: trunk cell

value: 10 day post fertilization


title: 20_b6129svcba_no.mcm


title: 5719882002_E_XY-Sry_E

value: XY-Sry

value: 75 days


title: MKL-1 Vehicle IgG - Rep 1

value: 1:100 rabbit anti-mouse IgG (Abcam ab46540)


title: Neg-Ctrl-1

description: SMART-seq HT Kit


title: 19_b6129svcba_no.mcm


title: 5613703020_B_XY-Sry_E


title: 18_b6129svcba_no.mcm


title: WGC-14d-2_S5

description: Quartz-Seq

source_name: Germ cells

value: Germ cells

value: 14 day post fertilization


title: MKL-1 D12 EPZ011989 - Rep 2

data_processing:
Illumina basecalling was performed by Novogene.
Read quality was checked by FastQC.
Salmon version 1.2.0 was used to map the reads to GRch38p.13 version 101 cDNA with gDNA used as a decoy, and quantify transcript abundance.
tximport version 1.18.0 was used with the latest Ensembl human transcript database to generate files for use by DESeq2. Analysis was restricted to transcripts with both an Ensembl ID and an HGNC gene symbol.
DESeq2 was used to generate normalized transcript count file and perform comparisons between treatment conditions.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table contains normalized transcript counts for all samples calculated by DESeq2. All _quant.txt files contain Salmon quantification of each sample's transcript abundance.

extract_protocol:
Total RNA was extracted using a standard TRIzol/chloroform protocol.
mRNA libraries were generated using polyA capture and standard Illumina library preparation protocols.

treatment_protocol: Cells were plated at 12E4 cells/mL with 1% ethanol or 3 µM EPZ011989 in a final concentration of 1% ethanol. Cells were split approximately 1:2 into larger dishes with complete media refreshment every 3 days.

value: 3 µM EPZ011989 in 1% ethanol

tag: day


title: 5613703028_B_XXSry_B

value: Blank

value: XXSry


title: ZGC-14_S2

description: Quartz-Seq


title: 5719882029_C_XY-Sry_E

value: liver


title: 5719882030_G_XY-Sry_T

value: Testosterone


title: 5719882028_B_XY-Sry_T


title: 17_b6129svcba_no.mcm

extract_protocol:
snHi-C protocol according to Flyamer et al., 2017.
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) or MPIB NGS Core facility (https://www.biochem.mpg.de/7076201/NGS) following the standard DNA sample preparation protocol.

value: wild type

value: maternal


title: 5719882013_H_XY-Sry_T


title: 22_b6129svcba_no.mcm

value: paternal


title: 16_b6129svcba_no.mcm

value: G1 zygote


title: WGC-14d_S4

description: Quartz-Seq

value: Nadia/Tupfel long-fin hybrid


title: MKL-1 D12 EPZ011989 - Rep 1


title: ZGC-12d_S1

description: Quartz-Seq

value: 12 day post fertilization


title: Eca109_before Interference_replicate 1 [NC-1]

value: esophageal squamous cell carcinoma cell line

value: control


title: MKL-1 Vehicle IgG - Rep 2

value: 1% ethanol


title: MKL-1 D12 Vehicle - Rep 3


title: 15_b6129svcba_no.mcm


title: 5719882006_C_XY-Sry_T

value: XY-Sry

value: 75 days


title: MKL-1 D12 Vehicle - Rep 2


title: MKL-1 D12 Vehicle - Rep 1


title: 14_b6129svcba_no.mcm


title: WGC-12d_S3

description: Quartz-Seq

value: Germ cells


title: WGC-12d-2_S6

description: Quartz-Seq


title: 5719882006_G_XY-Sry_E

value: Estradiol


title: MKL-1 D12 EPZ011989 - Rep 3

value: 3 µM EPZ011989 in 1% ethanol


title: 5613703028_E_XY-Sry_T


title: MKL-1 D6 EPZ011989 - Rep 3


title: ZGC-12d-4

description: SMART-seq HT Kit


title: 5719882030_C_XY-Sry_B

value: Blank


title: 5719882002_A_XY-Sry_B

value: liver


title: ZGC-12d-3

description: SMART-seq HT Kit


title: MKL-1 D6 EPZ011989 - Rep 2


title: 11_b6129svcba_no.mcm


title: ZGC-12d-2

description: SMART-seq HT Kit


title: MKL-1 D6 Vehicle - Rep 3


title: 9_b6129svcba_wt.ctrl


title: 5719882013_D_XY-Sry_B


title: ZGC-12d-1

description: SMART-seq HT Kit


title: 5613703020_F_XY-Sry_B


title: MKL-1 D6 Vehicle - Rep 2


title: WGC-12d-4

description: SMART-seq HT Kit


title: X5773660134_A_XX_E

value: XX

value: inguinal adipose


title: 8_b6129svcba_wt.ctrl

value: wild type


title: 5613703028_A_XXSry_B

value: XXSry


title: WGC-12d-3

description: SMART-seq HT Kit


title: MKL-1 D6 Vehicle - Rep 1


title: HP3 germinal center B cells

city: New York

first: Michel

last: Nussenzweig

state: NY

address: 1230 York Ave

institute: Rockefeller University

description: 10x Genomics single cell VDJ RNA experiment

data_processing:
B cell receptor transcripts were assembled using Cell Ranger v6.0.1
Genome_build: custom hybrid reference using created by combining pre-selected knocked-in V(D)J genes from GRCh38 with the complete V(D)J reference from GRCm38
Supplementary_files_format_and_content: fasta file contains the assembled VDJ contigs
Supplementary_files_format_and_content: csv file contains the VDJ annotation of the assembled contigs

source_name: spleen and mesenertic lymph nodes

extract_protocol:
Sorted germinal center B cells were counted in the final injection volume, and 18,000 cells loaded onto a Chromium Controller (10x Genomics).
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5 v2 Reagent Kit (PN-1000265) according to manufacturer’s protocol. Chromium Single Cell Mouse BCR Amplification Kit (PN-1000255) was used for VDJ cDNA amplification. After QC, 5’ expression and VDJ Libraries were pooled 1:1 and sequenced on an Illumina NOVAseq S1 flowcell at the Rockefeller University Genomics Core.

tag: background strain

value: spleen and mesenertic lymph nodes

value: germinal center B cells


title: 7_b6129svcba_wt.ctrl

data_processing:
Base calling was performed by VBCF NGS unit or MPIB NGS Core facility.
Mapping: Iterative mapping (see Imakaev et al., 2012) using bwa.
Read filtering was performed as in Flyamer et al., 2017.
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.

value: maternal

value: G1 zygote


title: 13_b6129svcba_no.mcm


title: U2OS_SI-3

city: Beijing

first: Xiaohan

last: Yang

address: 38 Xueyuan road

department: Biochemistry and Biophysics

institute: Peking Unversity Health Science Center

data_processing:
STAR was used to align clean reads to reference genome. Volcano Plots were drawn by the R based on the differentially gene analysis and the color was determined by the filtering criteria. Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of differentially expressed genes. Pathway analysis was used to find out the significant pathway of the genes according to KEGG database. ClusterProfiler was applied to identify the significant GO categories and select the significant pathway, and the threshold of significance was defined by p-value and FDR.
Supplementary_files_format_and_content: txt files including all genes abundance, differential genes and statistic method.

source_name: U2OS SI

extract_protocol:
Total cellular RNAs were prepared and RNA-sequencing was performed.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: U2OS cells were transfected with control or LSD1 siRNAs for 48 h.

value: siRNA transfection

value: LSD1 knockdown


title: 6_b6129svcba_wt.ctrl

source_name: zygote pronucleus

value: paternal


title: X5773660159_E_XX_E

extract_protocol: RNA from liver and inguinal adipose tissue was isolated using Trizol (Invitrogen, Carlsbad, CA). After homogenization and centrifugation, chloroform was applied for further RNA extraction based on the protocol provided by Invitrogen.

value: 75 days


title: WGC-12d-1

description: SMART-seq HT Kit

value: Nadia/Tupfel long-fin hybrid

value: Germ cells

value: 12 day post fertilization


title: TNF-Tg

city: Rochester

first: H. Mark

last: Kenney

state: New York

address: 601 Elmwood Ave, Box 665

department: Center for Musculoskeletal Research

institute: University of Rochester Medical Center

description: TNF-Tg 9-months

data_processing:
Demultiplexing: cellranger 3.1 mkfastq --use-bases-mask y*,I8,y* --nopreflight
Counting: cellranger-3.1.0 count --fastqs=./fastq_path --jobmode=slurm --maxjobs=100 --nopreflight --transcriptome=refdata-cellranger-mm10-3.0.0/ --project=${PROJECT} --indices=SI-GA-${INDEX} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX}
To evaluate changes in cell composition between WT and TNF peripheral vasculature, we integrated these datasets and performed unsupervised clustering using the Seurat R package (v.4.0.3). Various tdT1, tdT2, and WT integrations were performed with supervised clustering based on the clustering derived from the WT and TNF integration. The filtered feature/barcode matrices were imported using Seurat, and the vignette for introduction to scRNAseq integration was followed.
Genome_build: mm10
Supplementary_files_format_and_content: cell barcodes (_barcodes.tsv), feature list (_features.tsv), and feature/barcode matrices (_matrix.mtx) are provided for each condition

source_name: TNF-Tg 9-months Peripheral Vasculature

extract_protocol:
Evan's blue dye was administered intradermal into the mouse hindpaw to identify the two popliteal lymphatic vessels that run on either side of the superficial saphenous vein in the back of the calf draining into the popliteal lymph node behind the knee. All three vessels were dissected, manually and enzymatically digested (Accumax; Innovative Cell Technologies Cat# AM-105) for 1h at room temperature, filtered with a 75um strainer, and single cell suspensions were sorted by fluorescence activated cell sorting based on tdTomato fluoresence (tdT1 & tdT2) or scatter profile (WT and TNF). Sorted cells were then submitted to the Genomics Research Center at the University of Rochester for library preparation and sequencing. All cells in each sample were loaded on a Chromium Single-Cell Insrument (10x Genomics) and single-cell Gel Bead-in-Emulsions were generated. The Chromium Single-Cell 3' Library & Gel Bead Kit (10x Genomics) was used to generate the library based on the manufacturer's instructions. Barcoded cDNA from the Gel Bead-in-Emulsions was purified with DynaBeads MyOne Silane Beads (ThermoFisher Scientific Cat# PN37002D) with PCR amplification for 3' cDNA library construction. NextSeq 550 (tdT1) and NovaSeq 6000 (tdT2, WT, TNF) Illumina sequencers generated the sequenced data.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TNF-Tg 9-months


title: U2OS_SI-2


title: 12_b6129svcba_no.mcm

city: Vienna

last: Dequeker

address: Dr. Bohr-Gasse 3

institute: IMBA - Institute of Molecular Biotechology


title: WGC-12d-2

description: SMART-seq HT Kit


title: U2OS_SI-1


title: Wild-Type

description: Wild-Type C57BL6 9-months

source_name: Wild-Type C57BL6 9-months Peripheral Vasculature

value: Wild-Type C57BL6 9-months


title: 5_b6129svcba_wt.ctrl


title: ZGC-10d-3

description: SMART-seq HT Kit

value: 10 day post fertilization


title: MKL-1 D6 EPZ011989 - Rep 1

value: 3 µM EPZ011989 in 1% ethanol


title: tdTomato 2

description: tdTomato Enriched 2

source_name: CSPG4-Cre;tdTomato Enriched 2 Peripheral Vasculature

value: tdTomato Enriched 2


title: 4_b6129svcba_wt.ctrl

value: wild type


title: ZGC-10d-2

description: SMART-seq HT Kit


title: U2OS_NC-2

value: control


title: U2OS_NC-3


title: 10_b6129svcba_no.mcm


title: Lepr-after IR

first: min

last: Deng

address: Beijing HaiDian District, Mingyuanxilu No.2

institute: China Agricultural University

description: Lepr-after IR

data_processing:
Chromium Single Cell 3’ v2 libraries were sequenced with a Novaseq 6000 sequencer, with the following sequencing parameters: read 1, 150 cycles; i7 index, 8 cycles and read 2, 150 cycles.
Raw Illumina data were demultiplexed and processed using Cell Ranger (10X Genomics version Cell Ranger 2.0.1)
In order to remove partial cells and doublets, cells with less than 350 genes or more than 5000 genes were removed.
Cells with more than 10% of mitochondrial unique molecular identifiers (UMIs) were removed, as a high proportion of mitochondrial expression in cells is indicative of cell stress/damage during isolation.
Genome_build: mm10

source_name: intestinal mesenchymal cells

extract_protocol:
Intestinal mesenchymal were digested into single cells, the Epcam-CD45-fvd450- cells were sorted by FACS. for Lepr+cells,the GFP+ cells were sorted by FACS.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v2 chemistry. Cell capture, library preparation, quality control, and sequencing was performed at beijing capitalBio technology
Single Cell 3’ v2 chemistry - 10X Genomics

treatment_protocol: untreat

value: Lepr-after IR

value: 8 wks

value: untreat

tag: genetype

value: Lepr-Cre; R26-mTmG


title: Lepr-before IR

description: Lepr-before IR

value: Lepr-before IR


title: ZGC-10d-1

description: SMART-seq HT Kit


title: 2_b6129svcba_no.mcm

first: Bart

tag: genotype

value: paternal

value: G1 zygote


title: U2OS_NC-1

value: siRNA transfection


title: WGC-10d-3

description: SMART-seq HT Kit

tag: strain

value: Nadia/Tupfel long-fin hybrid

value: Germ cells


title: 3_b6129svcba_no.mcm

tag: parental origin

value: maternal


title: WGC-10d-2

description: SMART-seq HT Kit


title: Whole mesenchymal cells

description: Whole mesenchymal cells

tag: cell type

value: Whole mesenchymal cells

value: WT mice


title: MCM2-AID_Aux

description: Proximity ligated gDNA

data_processing:
Base calling was performed by VBCF NGS unit or MPIB NGS Core facility
Data were processed using distiller-nf pipeline using this project.yml file: https://gist.github.com/Phlya/3dc64b6152bbcd9d7a2f52ccf22ad35f
Genome_build: hg38
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 2kb, 5kb,10kb, 25kb, 50kb, 100kb, 250kb, 500kb and 1Mb resolutions stored in the mcool file format. Also, pair files describing detected deduplicated interacting pairs.

source_name: HCT116 MCM2-AID

extract_protocol:
Hi-C was performed largely as described in Rao et al, 2014 with minor modifications. Briefly, ~5x10 6 HCT116 cells were crosslinked in 1% formaldehyde for 10 min at RT, snap-frozen and stored at -80°C. After permeabilization in lysis buffer (0.2% Igepal, 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 1x Halt Protease inhibitor cocktail) nuclei were isolated in 0.3% SDS in NEBuffer 3 at 62°C for 10 min. SDS was quenched with 1% Triton X-100 at 37°C for 1 h, then the nuclei were pelleted and resuspended in 250 μl DpnII buffer with 600 U DpnII (New England Biolabs) at 37˚C. After overnight digestion, 200 U DpnII were added for 2 h more incubation. Then, the ends were filled-in with d(G/C/T)TPs and biotin-14-dATP (Life Technologies) using Klenow (New England Biolabs) for 1.5 h at 37°C. After ligation at room temperature for 4 h with T4 ligase (New England Biolabs), the nuclei were spun down, resuspended in 200 μl mQ and digested with proteinase K for 30 min at 55°C in presence of 1% SDS. Cross-links were reversed at 65°C overnight after addition of NaCl to a final concentration of 1.85 M. After ethanol precipitation and a 70%–80% ethanol wash, DNA was resuspended in 50 µl of 10 mM Tris EDTA, incubated on ice for 15 min and then sheared to ~300-1300 bp fragments using the E220 Focused-ultrasonicator (Covaris). DNA was bound to MyOne C1 Streptavidin beads (ThermoFischer) and used for library preparation with the NEB Next Ultra Library Prep kit (Illumina). Libraries were sequenced on the NovaSeq 6000 system with 100 bp paired-end reads (at VBCF NGS Unit)
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) or MPIB NGS Core facility (https://www.biochem.mpg.de/7076201/NGS) following the standard DNA sample preparation protocol.

value: Auxin


title: 1_b6129svcba_no.mcm


title: mouseLiver_rep2_atac

city: Pittsburgh

first: Morgan

last: Wirthlin

state: Pennsylvania

address: 4400 Fifth Ave

department: Computational Biology

institute: Carnegie Mellon University

data_processing:
ATAC-seq alignment: Reads were mapped to the mm10 or rn6 genome using the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline).
ATAC-seq filtering: Duplicate reads, mitochondrial reads, and multi-mapping reads were filtered out as a part of the ENCODE ATAC-seq pipeline. We made the following read filtering changes from the pipeline defaults: "atac.multimapping" : 0.
ATAC-seq peak calling: Peaks were called on each sample individually using MACS2 within the ENCODE ATAC-seq pipeline workflow. We made the following changes from pipeline defaults: "atac.cap_num_peak" : 300000 and "atac.smooth_win" : 150.
ATAC-seq peak filtering: Reproducible peaks among replicates were determined within the ENCODE ATAC-seq pipeline workflow using IDR with the following changes from pipeline defaults: "atac.enable_idr" : true and "atac.idr_thresh" : 0.1.
Other: More information on all data processing and conclusions can be found in the publication.
Genome_build: mm10, rn6
Supplementary_files_format_and_content: ATAC-seq peaks called in each sample
Supplementary_files_format_and_content: MACS2 pval signal tracks for each sample in bigwig format

source_name: adult male mouse liver

extract_protocol:
Nuclei were extracted from fresh tissue with Dounce homogenization in lysis buffer. The nuclei were pelleted by centrifugation and filtered through 70µm and 40µm strainers.
ATAC-seq libraries were constructed with standard amplification and size selection methods. See publication for more details.

treatment_protocol: Mice were injected intravenously with an fluorescent AAV related to tissues for a different study. The procedure was minimally invasive and did not affect the health of the animals. Rats received no treatments.

value: liver

tag: sample type

value: bulk tissue

tag: Sex

value: M

value: 72 days

tag: sequenced molecule

value: transposase-accessible DNA


title: MCM2-AID_DMSO

description: Proximity ligated gDNA

value: DMSO


title: tdTomato 1

description: tdTomato Enriched 1

source_name: CSPG4-Cre;tdTomato Enriched 1 Peripheral Vasculature

value: tdTomato Enriched 1


title: WGC-10d-1

description: SMART-seq HT Kit

value: 10 day post fertilization


title: mouseLiver_rep1_atac

source_name: adult female mouse liver

value: F


title: B2_I3E3SRS_rep2

status: Public on Mar 06 2022

city: Berkeley

first: Xinyi

last: Zhang

address: 327 Stanley Hall

institute: UC Berkeley

data_processing:
Reads were quantified by Salmon (Patro et al. 2017) using a mouse reference transcriptome, ensembl GRCm3817
Transcript-level quantification were aggregated to gene level through tximport package (Soneson et al.2015), and "lengthScaledTPM" option was used.
Supplementary_files_format_and_content: ".sf" output of Salmon

source_name: mouse neuroblastoma cells (N2A)

growth_protocol: Neuro2A cells (N2A; UCB Cell Culture Facility) were cultured in T25 flasks using standard cell culture conditions for all experiments - 37 oC, 5% CO2, and complete growth medium consisting of DMEM (Gibco™ 10566016), 10% FBS (Avantor Seradigm 89510), and 1% penicillin-streptomycin (Gibco™ 15140122). Cells were grown to approximately 80-90% confluency and one day prior to each imaging experiment, they were resuspended and seeded into 384 glass-bottom well plates (Corning 4581) for RNA-seq. At the start of each RNA-seq experiment, the confluency was approximately 70%.

extract_protocol:
We followed the manufacturer’s protocol for RNA extraction (Qiagen RNeasy Mini Kit).
We followed the manufacturer’s protocol for library preparation (NEBNext Ultra II RNA library prep kits for Illumina).

treatment_protocol: N2A cells were either subject to the specific laser irradiation condition as described in our manuscript or were not exposed to laser.

value: Exposure to laser irradiation condition I3-E3-SRS

tag: batch id


title: B2_I3E3SRS_rep1


title: B2_NC_rep2

value: Unexposed


title: B2_I3E3SRS_rep3


title: B2_NC_rep1


title: B1_I2E2_rep3

value: Exposure to laser irradiation condition I2-E2


title: B1_I2E2_rep2


title: B1_I2E2_rep1


title: B1_I0E4_rep3

value: Exposure to laser irradiation condition I0-E4


title: B1_I0E4_rep2


title: B1_I0E4_rep1


title: B1_I0E2_rep2

value: Exposure to laser irradiation condition I0-E2


title: B1_I0E2_rep1


title: B1_I0E0_rep3

value: Exposure to laser irradiation condition I0-E0


title: B1_NC_rep3


title: B1_NC_rep2


title: B1_I0E0_rep2


title: B1_I0E0_rep1


title: 3D7_WT_S_input, Rep1

city: Shanghai

first: Mei

last: Jiang

state: Shanghai

address: 1239 Siping Road

institute: Tongji University

data_processing:
To remove residual adapters and low-quality bases, sliding window trimming was performed on reads with Trimmomatic v0.39 using a window size of 4 and average quality of the window above 15. A minimum read length of 50 bp and average read quality above 20 were required after read clipping.
Trimmed ChIP-seq reads were mapped to the P. falciparum 3D7 reference genome (release 47) using Bowtie2 v2.4.2 and default parameters.
Peaks were identified using the callpeak function of MACS2 v2.2.7.1 and a q-value cutoff of 0.05. The options --call-summits and --broad were applied to the detection of PfApiAP2 and PfHP1 binding peaks, respectively. Peaks with fold enrichment below 1.5 were removed from downstream analysis. Furthermore, a transfectant with episomal GFP expression was used as a negative control to exclude ChIP background signals of the anti-GFP antibody. PfApiAP2 binding peaks with their fold enrichment/background GFP fold enrichment lower than 1.5 were also removed from further studies.
Normalized signal tracks of log2-transformed ChIP/input fold enrichment were generated with MACS2 bdgcmp function.
Genome_build: Pf 3D7 v47
Supplementary_files_format_and_content: bigWig files of log2-transformed ChIP/input fold enrichment
Supplementary_files_format_and_content: BED files of peak summits for PfApiAP2 ChIP-seqs
Supplementary_files_format_and_content: BED files of peaks for PfHP1 ChIP-seqs

organism: Plasmodium falciparum

source_name: schizont (40-45 hpi)

growth_protocol: Parasites were cultured in fresh O-type human erythrocytes in complete RPMI 1640 medium (Gibco) with 0.5% Albumax I (Invitrogen) and a gas phase maintained under 5% CO2, 5% O2 and 90% N2 at 37°C.

extract_protocol:
Synchronized parasites were harvested at the ring (10-15 hpi), trophozoite (25-30 hpi), and schizont (40-45 hpi) stages respectively and crosslinked immediately with 1% paraformaldehyde (Sigma) by rotating for 10 minutes at 37°C, which was then quenched with 0.125 M glycine for 5 minutes on ice. Parasite nuclei released from infected red blood cells were sheared for 20-30 minutes using an M220 sonicator (Covaris) at 5% duty cycle, 200 cycles per burst, and 75 W of peak incident power to generate 100-500 bp fragments in length. 20 µL of the sheared chromatin was reserved as the input control. Chromatin was subsequently immunoprecipitated overnight at 4°C using 0.5 µg of antibodies against GFP (Abcam, ab290) or HP1 and protein A/G magnetic beads (ThermoFisher Scientific, 26162). After extensive washes, the immunoprecipitated materials were eluted with elution buffer. Then crosslinking was reversed by overnight incubation at 45°C, followed by treatments of RNase A at 37°C for 30 minutes and Proteinase K at 45°C for two hours. The ChIPped DNA was finally purified according to the MinElute PCR purification kit (Qiagen, 28006) instructions.
1.5 ng of ChIP-DNA was subjected to end-repair (Epicentre, ER81050), 3' adenylation (NEB, M0212L), and adapter ligation (NEB, M2200L). Then after purification with Agencourt AMPure XP beads (Beckman Coulter), libraries were amplified using the KAPA HiFi PCR Kit (KAPA Biosystems, KB2500) under the following conditions: 1 minute of initial denaturation at 98°C, 12 cycles of 10 seconds at 98°C and 1 minute at 65°C, and 5 minutes of final extension at 65°C.

treatment_protocol: Ring stage cultures were regularly synchronized by treatments of 5% sorbitol.

value: whole body

tag: developmental stage

value: schizont (40-45 hpi)

value: Pf 3D7

value: wild type

tag: host

value: Homo sapiens

tag: chip antibody


title: 3D7_WT_S_HP1_ChIP-seq, Rep1

tag: tissue


title: 3D7_WT_S_input, Rep2


title: 3D7_WT_S_HP1_ChIP-seq, Rep2


title: 3D7_WT_T_input, Rep1

source_name: trophozoite (25-30 hpi)

value: trophozoite (25-30 hpi)


title: 3D7_WT_T_input, Rep2


title: 3D7_WT_T_HP1_ChIP-seq, Rep1


title: 3D7_WT_R_input, Rep2

source_name: ring (10-15 hpi)

value: ring (10-15 hpi)


title: 3D7_WT_R_input, Rep1


title: 3D7_WT_T_HP1_ChIP-seq, Rep2


title: 3D7_WT_R_HP1_ChIP-seq, Rep1


title: 3D7_GFP_S_input

value: GFP


title: 3D7_WT_R_HP1_ChIP-seq, Rep2


title: 3D7_GFP_S_GFP_ChIP-seq, Rep2

value: anti-GFP (Abcam, ab290)


title: 3D7_AP2-O5-GFP_S_AP2-O5_ChIP-seq, Rep2


title: 3D7_GFP_S_GFP_ChIP-seq, Rep1


title: 3D7_AP2-O5-GFP_T_input


title: 3D7_AP2-O5-GFP_S_AP2-O5_ChIP-seq, Rep1


title: 3D7_AP2-O5-GFP_S_input


title: 3D7_AP2-O5-GFP_T_AP2-O5_ChIP-seq, Rep2


title: 3D7_AP2-O5-GFP_T_AP2-O5_ChIP-seq, Rep1


title: 3D7_AP2-O5-GFP_R_input


title: B1_I0E2_rep3

tag: treatment


title: 3D7_AP2-O5-GFP_R_AP2-O5_ChIP-seq, Rep2


title: 3D7_AP2-O5-GFP_R_AP2-O5_ChIP-seq, Rep1


title: 3D7_AP2-O2-GFP_S_input


title: 3D7_AP2-O2-GFP_S_AP2-O2_ChIP-seq, Rep2


title: 3D7_AP2-O2-GFP_S_AP2-O2_ChIP-seq, Rep1


title: B1_NC_rep1


title: 3D7_AP2-O2-GFP_T_input


title: 3D7_AP2-O2-GFP_T_AP2-O2_ChIP-seq, Rep2


title: 3D7_AP2-O2-GFP_T_AP2-O2_ChIP-seq, Rep1


title: 3D7_AP2-L-GFP_S_input


title: 3D7_AP2-L-GFP_S_AP2-L_ChIP-seq, Rep1


title: 3D7_AP2-L-GFP_T_input


title: 3D7_AP2-L-GFP_T_AP2-L_ChIP-seq, Rep1


title: 3D7_AP2-L-GFP_R_input


title: 3D7_AP2-L-GFP_R_AP2-L_ChIP-seq, Rep2


title: 3D7_AP2-HS-GFP_T_input


title: 3D7_AP2-L-GFP_R_AP2-L_ChIP-seq, Rep1


title: 3D7_AP2-HS-GFP_S_AP2-HS_ChIP-seq, Rep2


title: 3D7_AP2-HS-GFP_R_input


title: 3D7_AP2-HS-GFP_S_input


title: 3D7_AP2-HS-GFP_T_AP2-HS_ChIP-seq, Rep1


title: 3D7_AP2-HS-GFP_T_AP2-HS_ChIP-seq, Rep2


title: 3D7_AP2-HC-GFP_S_input


title: 3D7_AP2-HC-GFP_S_AP2-HC_ChIP-seq, Rep2


title: 3D7_AP2-HC-GFP_S_AP2-HC_ChIP-seq, Rep1


title: 3D7_AP2-HC-GFP_T_input


title: 3D7_AP2-HC-GFP_T_AP2-HC_ChIP-seq, Rep2


title: 3D7_AP2-HC-GFP_R_input


title: 3D7_AP2-HC-GFP_R_AP2-HC_ChIP-seq, Rep2


title: 3D7_AP2-G5-GFP_S_input


title: 3D7_AP2-HC-GFP_R_AP2-HC_ChIP-seq, Rep1


title: 3D7_AP2-G5-GFP_S_AP2-G5_ChIP-seq, Rep2


title: 3D7_AP2-G5-GFP_S_AP2-G5_ChIP-seq, Rep1


title: 3D7_AP2-G5-GFP_T_AP2-G5_ChIP-seq, Rep2


title: 3D7_AP2-G5-GFP_T_input


title: 3D7_AP2-G5-GFP_R_input


title: 3D7_AP2-L-GFP_T_AP2-L_ChIP-seq, Rep2


title: 3D7_AP2-G5-GFP_T_AP2-G5_ChIP-seq, Rep1


title: 3D7_AP2-G5-GFP_R_AP2-G5_ChIP-seq, Rep2


title: 3D7_AP2-L-GFP_S_AP2-L_ChIP-seq, Rep2


title: 3D7_AP2-G5-GFP_R_AP2-G5_ChIP-seq, Rep1


title: 3D7_AP2-G3-GFP_S_input


title: 3D7_AP2-G4-GFP_S_AP2-G4_ChIP-seq, Rep1


title: 3D7_AP2-G4-GFP_S_input


title: 3D7_AP2-G4-GFP_S_AP2-G4_ChIP-seq, Rep2


title: 3D7_AP2-G3-GFP_S_AP2-G3_ChIP-seq, Rep2


title: 3D7_AP2-G3-GFP_S_AP2-G3_ChIP-seq, Rep1


title: 3D7_AP2-G3-GFP_T_input


title: 3D7_AP2-HS-GFP_S_AP2-HS_ChIP-seq, Rep1


title: 3D7_AP2-HS-GFP_R_AP2-HS_ChIP-seq, Rep1


title: 3D7_AP2-HS-GFP_R_AP2-HS_ChIP-seq, Rep2


title: 3D7_AP2-G3-GFP_T_AP2-G3_ChIP-seq, Rep1


title: 3D7_AP2-G3-GFP_T_AP2-G3_ChIP-seq, Rep2


title: 3D7_AP2-G3-GFP_R_input


title: 3D7_AP2-G3-GFP_R_AP2-G3_ChIP-seq, Rep2


title: 3D7_AP2-G3-GFP_R_AP2-G3_ChIP-seq, Rep1


title: 3D7_AP2-G2-GFP_S_input


title: 3D7_AP2-G2-GFP_S_AP2-G2_ChIP-seq, Rep2


title: 3D7_AP2-G2-GFP_T_input


title: 3D7_AP2-HC-GFP_T_AP2-HC_ChIP-seq, Rep1


title: 3D7_AP2-G2-GFP_S_AP2-G2_ChIP-seq, Rep1


title: 3D7_AP2-G2-GFP_T_AP2-G2_ChIP-seq, Rep2


title: 3D7_AP2-G2-GFP_R_AP2-G2_ChIP-seq, Rep2


title: 3D7_AP2-G2-GFP_R_input


title: 3D7_AP2-exp-GFP_S_input


title: 3D7_AP2-exp-GFP_S_AP2-exp_ChIP-seq, Rep2


title: 3D7_AP2-exp-GFP_S_AP2-exp_ChIP-seq, Rep1


title: 3D7_AP2-G2-GFP_R_AP2-G2_ChIP-seq, Rep1


title: 3D7_AP2-exp-GFP_T_input


title: 3D7_AP2-exp-GFP_R_input


title: 3D7_AP2-12-GFP_S_AP2-12_ChIP-seq, Rep2


title: 3D7_AP2-12-GFP_S_input


title: 3D7_AP2-12-GFP_T_input


title: 3D7_AP2-exp-GFP_R_AP2-exp_ChIP-seq, Rep2


title: 3D7_AP2-exp-GFP_T_AP2-exp_ChIP-seq, Rep2


title: 3D7_AP2-exp-GFP_R_AP2-exp_ChIP-seq, Rep1


title: 3D7_AP2-exp-GFP_T_AP2-exp_ChIP-seq, Rep1


title: 3D7_AP2-12-GFP_R_input


title: 3D7_AP2-12-GFP_R_AP2-12_ChIP-seq, Rep2


title: 3D7_AP2-11B-GFP_S_AP2-11B_ChIP-seq, Rep1


title: 3D7_AP2-12-GFP_T_AP2-12_ChIP-seq, Rep1


title: 3D7_AP2-11B-GFP_T_AP2-11B_ChIP-seq, Rep2


title: 3D7_AP2-11B-GFP_S_AP2-11B_ChIP-seq, Rep2


title: 3D7_AP2-12-GFP_R_AP2-12_ChIP-seq, Rep1


title: 3D7_AP2-11B-GFP_T_input


title: 3D7_AP2-12-GFP_T_AP2-12_ChIP-seq, Rep2


title: 3D7_AP2-11B-GFP_R_AP2-11B_ChIP-seq, Rep1


title: 3D7_AP2-11A-GFP_S_input


title: 3D7_AP2-G2-GFP_T_AP2-G2_ChIP-seq, Rep1


title: 3D7_AP2-11B-GFP_S_input


title: 3D7_AP2-11B-GFP_T_AP2-11B_ChIP-seq, Rep1


title: 3D7_AP2-11A-GFP_T_AP2-11A_ChIP-seq, Rep2


title: 3D7_AP2-11B-GFP_R_AP2-11B_ChIP-seq, Rep2


title: 3D7_AP2-11A-GFP_R_AP2-11A_ChIP-seq, Rep2


title: 3D7_AP2-11A-GFP_S_AP2-11A_ChIP-seq, Rep2


title: 3D7_AP2-08-GFP_S_input


title: 3D7_AP2-12-GFP_S_AP2-12_ChIP-seq, Rep1


title: 3D7_AP2-08-GFP_S_AP2-08_ChIP-seq, Rep1


title: 3D7_AP2-08-GFP_T_AP2-08_ChIP-seq, Rep2


title: 3D7_AP2-11A-GFP_R_input


title: 3D7_AP2-11A-GFP_R_AP2-11A_ChIP-seq, Rep1


title: 3D7_AP2-08-GFP_R_AP2-08_ChIP-seq, Rep2


title: 3D7_AP2-11A-GFP_T_AP2-11A_ChIP-seq, Rep1


title: 3D7_AP2-08-GFP_S_AP2-08_ChIP-seq, Rep2


title: 3D7_AP2-08-GFP_T_input


title: 3D7_AP2-06B-GFP_T_input


title: 3D7_AP2-11B-GFP_R_input


title: 3D7_AP2-06B-GFP_R_AP2-06B_ChIP-seq, Rep2


title: 3D7_AP2-06A-GFP_S_input


title: 3D7_AP2-08-GFP_T_AP2-08_ChIP-seq, Rep1


title: 3D7_AP2-08-GFP_R_input


title: 3D7_AP2-11A-GFP_S_AP2-11A_ChIP-seq, Rep1


title: 3D7_AP2-11A-GFP_T_input


title: 3D7_AP2-06B-GFP_S_input


title: 3D7_AP2-06B-GFP_S_AP2-06B_ChIP-seq, Rep2


title: 3D7_AP2-08-GFP_R_AP2-08_ChIP-seq, Rep1


title: 3D7_AP2-O2-KO_S_RNA-seq, Rep2

data_processing:
To remove residual adapters and low-quality bases, sliding window trimming was performed on reads with Trimmomatic v0.39 using a window size of 4 and average quality of the window above 15. A minimum read length of 50 bp and average read quality above 20 were required after read clipping.
HISAT2 v2.2.1 was employed to align trimmed RNA-seq reads to the P. falciparum 3D7 reference genome (release 47) with the guide by the gene annotation, using default parameters except --max-intronlen 5000 --dta --rna-strandness RF.
StringTie v2.1.2 was used to count reads mapped to each gene.
Genome_build: Pf 3D7 v47
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every sample

extract_protocol:
Highly synchronous parasites were collected in TRIzol at the ring (10-15 hpi), trophozoite (25-30 hpi), and schizont (40-45 hpi) stages from the next cycle, respectively. Total RNA purification was conducted with the Direct-zol RNA Kit (Zymo Research).
Libraries were prepared for strand-specific RNA sequencing by poly(A) selection with the KAPA mRNA Capture Beads (KAPA Biosystems) first and then RNA fragmentation to a size of 300-400 nucleotides. Subsequent library preparation steps followed the protocol of the KAPA Stranded mRNA-seq Kit Illumina platform (KAPA Biosystems, KK8421).

treatment_protocol: Parasites were tightly synchronized to a 6-hour window by isolating schizonts over a 40% and 70% Percoll-sorbitol gradient followed by sorbitol treatment 6 hours post re-invasion.


title: 3D7_AP2-06B-GFP_S_AP2-06B_ChIP-seq, Rep1


title: 3D7_AP2-06B-GFP_T_AP2-06B_ChIP-seq, Rep2


title: 3D7_AP2-O2-KO_R_RNA-seq, Rep1


title: 3D7_AP2-06B-GFP_R_input


title: 3D7_AP2-06B-GFP_R_AP2-06B_ChIP-seq, Rep1


title: 3D7_AP2-06A-GFP_S_AP2-06A_ChIP-seq, Rep1


title: 3D7_AP2-O2-KO_T_RNA-seq, Rep2


title: 3D7_AP2-HS-KO_T_RNA-seq, Rep1


title: 3D7_AP2-O2-KO_S_RNA-seq, Rep1


title: 3D7_AP2-O2-KO_T_RNA-seq, Rep1


title: 3D7_AP2-HS-KO_S_RNA-seq, Rep2


title: 3D7_AP2-HS-KO_S_RNA-seq, Rep1


title: 3D7_AP2-HS-KO_T_RNA-seq, Rep2


title: 3D7_AP2-HS-KO_R_RNA-seq, Rep2


title: 3D7_AP2-HC-KO_S_RNA-seq, Rep2


title: 3D7_AP2-HC-KO_S_RNA-seq, Rep1


title: 3D7_AP2-HS-KO_R_RNA-seq, Rep1


title: 3D7_AP2-06B-GFP_T_AP2-06B_ChIP-seq, Rep1


title: 3D7_AP2-HC-KO_S_RNA-seq, Rep3


title: 3D7_AP2-HC-KO_R_RNA-seq, Rep2


title: 3D7_AP2-HC-KO_R_RNA-seq, Rep1


title: 3D7_AP2-HC-KO_T_RNA-seq, Rep2


title: 3D7_AP2-G5-KO_T_RNA-seq, Rep2


title: 3D7_AP2-HC-KO_T_RNA-seq, Rep3


title: 3D7_AP2-HC-KO_T_RNA-seq, Rep1


title: 3D7_AP2-G5-KO_S_RNA-seq, Rep1


title: 3D7_AP2-06A-GFP_S_AP2-06A_ChIP-seq, Rep2


title: 3D7_AP2-G5-KO_R_RNA-seq, Rep2


title: 3D7_AP2-O2-KO_R_RNA-seq, Rep2


title: 3D7_AP2-G5-KO_S_RNA-seq, Rep2


title: 3D7_AP2-G5-KO_R_RNA-seq, Rep1


title: 3D7_AP2-G4-KO_S_RNA-seq, Rep2


title: 3D7_AP2-HC-KO_R_RNA-seq, Rep3


title: 3D7_AP2-G5-KO_T_RNA-seq, Rep1


title: 3D7_AP2-G4-KO_S_RNA-seq, Rep1


title: 3D7_AP2-G4-KO_T_RNA-seq, Rep2


title: 3D7_AP2-G4-KO_T_RNA-seq, Rep1


title: 3D7_AP2-G2-KO_S_RNA-seq, Rep2


title: 3D7_AP2-G4-KO_R_RNA-seq, Rep2


title: 3D7_AP2-G2-KO_S_RNA-seq, Rep1


title: 3D7_AP2-G4-KO_R_RNA-seq, Rep1


title: 3D7_AP2-G2-KO_T_RNA-seq, Rep2


title: 3D7_AP2-G2-KO_R_RNA-seq, Rep1


title: 3D7_WT_S_RNA-seq, Rep3


title: 3D7_WT_S_RNA-seq, Rep2


title: 3D7_WT_S_RNA-seq, Rep1


title: 3D7_WT_T_RNA-seq, Rep3


title: 3D7_WT_T_RNA-seq, Rep2


title: 3D7_WT_R_RNA-seq, Rep3


title: s3-post

city: Hefei

first: Hao

last: Wang

state: Anhui

address: 81 Meishan Road

institute: Anhui Medical University

description: processed data file:  NAC sensitive breast cancer tissue.xlsx

data_processing:
FASTQ file quality control was performed using Trimmomatic (10), where N bases and low-quality (score <15) bases were removed. Reads aligning to rRNA and tRNA sequences were removed.
Quality control of the FASTQ file was performed by Trimmomatic. The N bases and low-quality (score <15) bases were trimmed. The reads belonging to rRNA and tRNA sequences were trimmed. The remaining reads were considered to be clean reads and were aligned to the human reference genome (hg19) with STAR v2.5.2b. The transcripts were quantified using RSEM and the expectation maximization algorithm was carried out to optimally assign reads that maps to multiple transcripts. The differential gene expression analysis was performed using DESeq2 R package.
Genome_build: Cleaned reads were aligned to the human reference genome (hg19) using STAR v 2.5.2b
Supplementary_files_format_and_content: FPKM

source_name: breast cancer tissue

extract_protocol:
Total RNA was extracted using the RNeasy FFPE Kit.
RNA sequencing libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems).
rRNA was first depleted with RiboErase, followed by DNase digestion for DNA removal. Purified RNA was subjected to first-strand cDNA synthesis, followed by second-strand synthesis with dUTP marking for strand specificity. This is followed by A-tailing, adapter ligation, and library amplification. Final library was  quantified using KAPA Library Quantification Kit (KAPA  Biosystems), and its fragment size distribution was analyzed  using a Bioanalyzer 2100 (Agilent).

value: NAC sensitive breast cancer tissue

value: FFPE

value: DOX and DTX-based treatment


title: s3-pre

value: untreated


title: s2-pre


title: 3D7_WT_R_RNA-seq, Rep1


title: s1-post


title: s2-post


title: R7-pre

description: processed data file:  NAC resistant breast cancer tissue.xlsx

value: NAC resistant breast cancer tissue


title: R7-post


title: R6-post


title: R6-pre


title: R5-post


title: R5-pre


title: R3-post


title: R4-pre


title: R2-post


title: R4-post


title: R3-pre


title: R1-post


title: R1-pre


title: M2DL4

city: Kalyani

first: Sreedhar

last: Chinnaswamy

state: WB

institute: National Institute of Biomedical Genomics

data_processing: Fastqc software was used to check the data quality of original sequencing data. TMM (trimmed mean of M-values) method in edgeR package was used to normalize the gene expression. The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 (35) and the gene expression level was estimated using RSEM v1.2.15. (36). Differentially expressed genes were identified using the edgeR program (37). Genes showing altered expression with p < 0.05 and more than 1.5-fold changes were considered differentially expressed.

source_name: Monocytes

growth_protocol: The cells were initially maintained in Promocell mononuclear medium, after revival they were transferred to RPMI-1640 medium supplemented with antibiotics and 10% FBS

extract_protocol:
Total RNA was isolated and sent to Quickbiology, Pasadena, CA, USA where RNA-seq and data analysis were carried out.
RNA integrity was checked using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and samples with clean rRNA peaks (RIN > 7) were used for further experiments. Library for RNA-seq was prepared according to KAPA stranded mRNA-Seq poly-A selected kit with a 201–300 bp insert size (KAPA Biosystems, Wilmington, MA, USA) using 250 ng total RNA as input. Final library quality and quantity were analyzed using an Agilent Technologies Bioanalyzer 2100 and Life Technologies Qubit 3.0 Fluorometer (Carlsbad, CA, USA). 150 bp paired-end reads were sequenced on an HiSeq 4000 (Illumina, San Diego, CA, USA).

treatment_protocol: The CD14+ cells were incubated with GM-CSF (for M1-MDM) or M-CSF (for M2-MDM) in presence or absence of IFN-λ3 (at 50 ng/ml) or IFN-λ4 (at 6 μg/ml) for six days, and then the cells were fully washed off any residual growth factors or IFNs.

value: Monocyte-derived macrophages

value: M-CSF

tag: ifn-l


title: 3D7_AP2-G2-KO_R_RNA-seq, Rep2


title: 3D7_AP2-G2-KO_T_RNA-seq, Rep1


title: M2DL3


title: M2CL4


title: 3D7_WT_T_RNA-seq, Rep1


title: M2BL3


title: M2BL4


title: M2AL3


title: M2AL4


title: M2BC

value: NT


title: M1DL4

value: GM-CSF


title: s1-pre


title: M1DL3


title: M1CL3


title: 3D7_WT_R_RNA-seq, Rep2

value: whole body


title: M1BL4


title: M1DC


title: M1CL4


title: mRNA_Wound7_2

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

data_processing:
Illumina Casava1.7 software used for basecalling.
miRNA-seq: The quality of raw data was assessed using FastQC v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used mapper.pl module in the miRDeep2 v0.1.3 package to filter low quality reads and remove sequencing adaptors and redundancies. Trimmed reads with length greater than 18 nt were mapped to GENCODE human reference genome (hg38) by the software Bowtie v1.2.2. The miRDeep2.pl module was then performed with default parameters to identify known miRNAs, which were compared to miRNAs in miRBase release 22.1. Counts of reads mapped to each known mature miRNAs were acquired from the quantifier.pl module output, without allowing mismatch.
Raw counts of  miRNAs were normalized for sequencing depth using TPM methods (transcript per million = mapped readcount / Total reads * 10e6).
mRNA-seq: Raw reads of mRNA sequencing were first trimmed for adaptors and low-quality bases using Trimmomatic v0.36 software. Clean reads were aligned to the human reference genome (GRCh38.p12), coupled with the comprehensive gene annotation file (GENCODEv31) using STAR v2.7.1a. Gene expression was then quantified by counting unique mapped fragments to exons using featureCount function from the Subread package.
Raw counts for each gene were normalized to fragments per kilobase of transcript, per million mapped reads (FPKM)-like values.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include miRNA TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw read counts for every miRNA and every sample
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample

source_name: Lower leg skin

extract_protocol:
The mRNA libraries were constructed with a total amount of 2 μg RNA per sample. Firstly, the ribosomal RNA was depleted by Epicentre Ribo-zero® rRNA Removal Kit (Epicentre). Subsequently, bulk strand-specific total-transcriptome RNA sequencing libraries were prepared by incorporating dUTPs in the second-strand synthesis step with NEB Next® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB). Finally, the libraries were sequenced on an Illumina Hiseq 4000 platform and 150 bp paried-end reads were generated for the following analysis.
paired-end 150bp

value: Skin

tag: gender

value: Male

tag: age

tag: patients

tag: ethnicity

value: Caucasian

tag: groups

value: Wound day 7

tag: librarytype

value: ribosomal RNA depletion


title: M1BC

tag: cell type


title: M1CC


title: M1BL3


title: M1AL4


title: M1AL3


title: M1AC


title: mRNA_Wound7_1

value: Female


title: mRNA_Wound1_5

value: Wound day 1


title: mRNA_Wound7_4


title: R2-pre

tag: sample type


title: mRNA_Wound1_3


title: mRNA_Wound7_3


title: mRNA_Wound1_1


title: M2CC


title: mRNA_Skin5

value: Intact skin


title: M2DC


title: mRNA_Wound1_2


title: M2CL3


title: mRNA_Wound1_4


title: mRNA_Skin3


title: mRNA_Skin2


title: mRNA_VU5

value: Venous ulcer


title: mRNA_VU4


title: mRNA_VU3


title: M2AC


title: mRNA_VU2


title: mRNA_VU1


title: TGS24 treated

city: Kolkata

first: Subhrangsu

last: Chatterjee

state: West Bengal

address: Kankurgachi

institute: Bose Institute

data_processing:
. The sequencing depth for each sample was 100 million reads. The raw reads were filtered using Trimmomatic (v-0.36) for retaining high-quality sequence and adapter trimming.
Other unwanted sequences, such as mitochondrial genome sequences, ribosomal RNAs, transfer RNAs, adapter sequences using Bowtie2 (2.2.4)
Filtered reads were aligned to Human genome (hg19) using splice aware aligner like STAR to quantify reads mapped to each transcript.
Total number of uniquely mapped read counts were estimated using FeatureCount (1.5.2). The raw read counts for control and treated samples were normalized using DESeq2.
A distribution of these log2(fold change) values were found to be normally distributed, wherein the genes which were found to be 2 standard deviation away from the mean (mean + 2×Standard deviation, mean- 2×Standard deviation) were differential expressed. GO annotation and Reactome pathway information for differentially  expressed genes were done using Panther database
Genome_build: hg19
Supplementary_files_format_and_content: heatmap generated using clustvis server

source_name: spheroid

growth_protocol: Human triple negative breast adenocarcinoma cell line, MDAMB-231 was procured from NCCS, Pune and was maintained in DMEM-complete media with 10% (v/v) FBS, 100 unit/ml penicillin, and 100 µg/ml streptomycin at 37ºC in a humidified incubator with 5% CO2.

extract_protocol:
RNA isolated from the samples using Trizol following manufacturer's protocol
using Illumina® HiSeq 4000/x platform to obtain 150-bp paired-end reads

treatment_protocol: One replicate of MDSMB231 spheroid was treated with TGS24

tag: cell line

value: breast cancer cell line MDA-MB-231

value: TGS24 treated


title: Control

value: Control


title: mRNA_Wound7_5


title: pGAL-RNY1 tRF Fu 2H ligation Rep 2

city: Worcester

first: Oliver

last: Rando

state: Massachusetts

address: 364 Plantation St

department: BMP

institute: University of Massachusetts

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt v2.9, when UMI was present reads were deduplicated with seqkit v0.14.0 and UMI sequence was trimmed with cutadapt.
Trimmed reads where then mapped to sacCer3 or mm10 with tRAX using default settings.
Genome_build: mm10, sacCer3
Supplementary_files_format_and_content: Each processed data file contains information about read-start/stop site, coveage, and  misinicorporation rate.

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: For full length tRNA experiments, yTG66 and yTG109 were grown overnight in selective synthetic media containing 2% dextrose, saturated cultures were diluted to OD600=0.1 and grown in selective synthetic media containing 2% dextrose until they reached OD600=0.5-07. For tRF experiments, yTG72 were grown overnight in selective synthetic media containing 2% raffinose. Saturated cultures were diluted to OD600=0.1 in selective synthetic media containing 2% raffinose and grown until early-midlog (OD600= 0.3-0.4). Cells were then centrifuged and diluted in selective synthetic media containing 2% galactose to an OD600 so that they reach OD600=0.5-0.7 in 360 minutes (“WT” samples were resuspended in selective synthetic media containing 2% galactose, centrifuged, and snap frozen immediately).

extract_protocol:
Mouse RNA was extracted using standard TRIZol protocol. Yeast RNA was extracted by beadbeating in TNE buffer (50 mM Tris-Cl pH7.4, 100 mM NaCl, 10 mM EDTA), followed by an acid Phenol extraction.
Libraries were constructed following published protocols.

tag: strain

tag: growth media

value: SC-Ura Galactose


title: WT tRF OTTR with 5' UMI Rep 2


title: pGAL-RNY1 tRF OTTR Rep 2


title: WT tRF Fu 2H ligation Rep 2


title: WT tRF Fu 16H ligation Rep 2


title: pGAL-RNY1 tRF OTTR with 5' UMI Rep 2


title: WT tRF OTTR Rep 2