title: KI-006


title: E3_DRB_E2C_Ribo

status: Public on Apr 19 2022

type: SRA

city: Beijing

first: Zhuqing

last: Xiong

state: FOREIGN

address: Haidian District

country: China

institute: School of Life Science, Tsinghua Univers

library_source: transcriptomic

data_processing:
Library strategy: Ribo-seq
Ribo-lite reads were trimmed with cutadapt v1.14 with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to mouse/human rRNAs sequences (mm9/hg19) using Bowtie2 v2.2.2 with parameters --seedlen=23. Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of mm9/hg19 using STAR v2.5.3a with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. The gene expression level was then calculated by Cufflinks v2.2.1 based on the annotation of CDS region。
All mRNA-seq data were trimmed by Trim Galore v0.4.2 then mapped to transcriptome of mm9/hg19 by STAR v2.5.3a with parameters --outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was calculated by Cufflinks v2.2.1.
Genome_build: mm9

molecule: total RNA

organism: Mus musculus

source_name: Preimplantation embryo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/47 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8557G).

treatment_protocol: PN5 zygotes were obtained and cultured in KSOM containing either 0.1% DMSO or 60 μM DRB (Sigma; D1916). DRB was washed it away at the early 2-cell stage and embryos were continued to be cultured in KSOM till late 8-cell stage.

tag: genotype

value: WT

tag: developmental stage

value: early 2-cell

tag: molecule

value: Ribosome protected fragment


title: O2_d11_CD13_Sendai_Exp1

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Reads were trimmed with Trim Galore (version 0.6.2) and aligned to the human genome (GRCh38) with Hisat2 (version 2.1.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: SeqMonk Annotated Probe reports of all genes with log2 RPM values in each sample

organism: Homo sapiens

source_name: Failing to reprogram fibroblast

growth_protocol: Human dermal fibroblasts were reprogrammed with the CytoTune™-iPS 2.0 Sendai Reprogramming kit (Invitrogen) as previously described (Milagre et al, 2017).

extract_protocol:
RNA was extracted alongside the genomic DNA with the AllPrep DNA/RNA mini kit (Qiagen).
Libraries were prepared as previously described (Milagre et al, 2017), and run on a Hiseq 2500 (Illumina) for 75 bp paired-end sequencing.

tag: cell type

value: Failing to reprogram fibroblast

tag: donor age

tag: days of reprogramming


title: PC-3, rBC2LCN-negative subpopulation_1

type: RNA

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression in human prostate cancer

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and 480 ng cRNA was hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray Kit (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software GX14.9.1 (Agilent) using default parameters.
Signal intensities of <1 were set to 1, and each chip was normalized to the 75th percentiles of all measurements from that chips. Baseline transformation of these data was not performed.

source_name: PC-3, passage 33, rBC2LCN-negative subpopulation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: PC-3 cells were maintained in F-12K medium (ATCC, 30-2004) supplemented with 10 % FBS (GIBCO, 12483-020) and 1 % Penstrep (SIGMA, I0516-5ML). The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was prepared by using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: PC-3 cells were separated into rBC2LCN-positive and -negative subpopulations by live cell sorting using HiLyte Fluor 647-conjugated rBC2LCN.

value: Human prostate cancer

tag: cell line

tag: passage number

tag: rbc2lcn status

value: negative


title: O2_d11_SSEA4_Sendai_Exp1

source_name: Reprogramming fibroblast

value: Reprogramming fibroblast


title: KI-007

city: Solna

first: Yizhou

last: Hu

state: Stockholm

address: C6 , Biomedicum Karolinska, Solnavägen 9,

country: Sweden

institute: Karolinska Institute

data_processing:
library strategy: single cell RNA-Seq: STRTseq
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis. In some reads, one of the three Gs has been replaced by an A by the Illumina HiSeq software, representing failed base calling at that position.
We rejected cells that had less than 2000 mRNA molecules, more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a separate cluster with no specific gene expression (putative damaged or dead cells). Genes that were detected at less than 4 molecules in the whole datasets were eliminated.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
Supplementary_files_format_and_content: HDF5 Loom file include raw counts and patient ID for each Sample

source_name: Glioma

growth_protocol: Surgical tissue samples of glioma patients were obtained in accordance with the protocol approved by regional ethical review board. Human glioblastoma tissues were minced with a scalpel, digested in Accutase/TrypLE (1:1) at 37°C for 15 min and triturated through 18 g and 21 g needles. The dissociated cells were resuspended in Neurocult NS-a basal medium (Stemcell) with addition of 1% B27 (Invitrogen), 0.5% N2 (Invitrogen), 10 ng/ml each of EGF and FGF2 (Peprotech) and plated on laminin-coated Primaria dishes (Corning) and cultured as adherent cells.

extract_protocol:
Fluidigm C1 Autoprep System  Cells medium (10-17 micrometer) microfluidic was used to capture the cells. 14 microlitre of cell suspension (approx. 800 cells/microlitre in N2 culturing medium with DNaseI) was mixed with 7 microlitre C1 Suspension Reagent after filtering. Single-cells were then captured for 30 min at 4°C. The protocol for Lysis, RT and PCR was performed as previously described  (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). Amplified cDNA was harvested with 13 microlitre Harvest Reagent and cDNA library quality was measured on an Agilent BioAnalyzer. Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase as described previously. 1 microlitre Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in 20 microlitre Binding and Blocking buffer (10mM Tris, 250mM NaCl, 5mM EDTA, 0.5% SDS) and added to each well. After 15 min incubation at room temperature, all wells were pooled, the beads washed once with 100 microlitre Washing buffer (10mM Tris-150mM NaCl, 0.02% Tween), once in 100 microlitre Qiagen Qiaquick PB and then twice using 100 microlitre Washing buffer. Restriction was performed to cleave fragments: the beads were incubated in 100 microlitre restriction mix (1x NEB CutSmart, 0.4 U/microlitre PvuI-HF enzyme) for 1h at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 microlitre to remove short fragments.
Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase (‘tagmentation’). 1 μl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in Binding and Blocking buffer (10 mM Tris, 250 mM NaCl, 5 mM EDTA, 0.5% SDS) at the ratio of 1:20 and then added to each well. After incubation at room temperature for 15 min, all wells were pooled, the beads washed once with 100 μl Washing buffer (10 mM Tris-150 mM NaCl, 0.02% Tween), once with 100 μl QIAGEN Qiaquick PB and then twice with 100 μl Washing buffer. Restriction was performed to cleave 3′ fragments: the beads were incubated in 100 μl restriction mix (1x NEB CutSmart, 0.4 U/μl PvuI-HF enzyme) for 1 hour at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in 30 μl ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 μl to remove short fragments. The molar concentrations of the libraries were determined with KAPA Library Quant qPCR (Kapa Biosystems) and size distribution was evaluated after PCR (12cycles) using an Agilent BioAnalyzer. Sequencing was performed on an Illumina HiSeq 2000 with C1-P1-PCR2 as read 1 primer and C1-TN5-U as index read primer. Reads of 50 bp as well as 8 bp index reads corresponding to the cell-specific barcodes were generated.

tag: tissue

value: Brain

tag: tissue type

value: Glioma

tag: age

value: IDH-wt

value: human glioblastoma cells


title: PC-3, rBC2LCN-negative subpopulation_2

source_name: PC-3, passage 34, rBC2LCN-negative subpopulation


title: PC-3, rBC2LCN-positive subpopulation_1

source_name: PC-3, passage 33, rBC2LCN-positive subpopulation

value: positive


title: 70925-34

first: Tong

last: Lian

address: Zhongguancun South Street

department: Biotechnology Research Institute

institute: CAAS

data_processing:
All libraries were sequenced using the Sanger method by Illumina 1.9 Platform. The adapters, low-quality reads, and the reads containing poly-N were removed to obtain clean reads
The clean-reads were mapped to Zea mays B73 genome by using Hisat software (v2.1.0) with setting non-strand-specific and other default parameters
The clean reads were assembled using Sam tools software, Cufflink software (v2.2.1) and Cuffcompare software (v2.2.1).
The counts were output using htseq-count(v0.11.2)
The annotation of genes refer to Zea mays B73 genome by Trinotate (v3.2.0).
Genome_build: Zea mays B73 genome
Supplementary_files_format_and_content: normalized_counts for each transcript and sample,  location of transcripts, annotation of transcripts

organism: Zea mays

source_name: DAN3130-Mature kernel

growth_protocol: DAN3130 and JI63 inbred lines are originated from China, belonging to the NSS subpopulation, JI63 with pedigree being (127-32 ×Tie84) × (Wei24 × Wei20) and DAN3130 with pedigree being American hybrid P78599. They were grown at Langfang, Hebei province, in the summer of 2018. Fresh kernel samples were collected on 24, 35 days after pollination then frozen in liquid nitrogen immediately. Mature kernel samples were harvested after all plants turned yellow. Three biological replicates of each stage were harvested.

extract_protocol:
Total RNA of DAP 24, DAP 35 and mature kernels were extracted using BAIXU Maize Kernel Total RNA Extraction Kit (Beijing, China). To eliminate any residual genomic DNA, total RNA was treated with RNase-free DNase I (New England Biolabs) and the concentration of RNA were determined using Nanodrop-2000. Total RNA was used to synthesize ﬁrst-strand complementary DNA (cDNA) using the RevertAid First Strand cDNA Synthesis kit (Fermentas).
RNA-Seq library preparation and sequencing were carried out by BEIJING BAIXU BIOTECH CO., LTD, Beijing, China. All libraries were sequenced using the Sanger method by Illumina 1.9 Platform. The adapters, low-quality reads, and the reads containing poly-N were removed to obtain clean reads. Then the clean-reads were mapped to Zea mays B73 genome by using Hisat software (v2.1.0) with setting non-strand-specific and other default parameters. Afterwards, the clean reads were assembled using Sam tools software, Cufflink software (v2.2.1) and Cuffcompare software (v2.2.1).

tag: cultivar

value: kernel

value: Mature kernel


title: E3_Ctr_E2C_smart

data_processing:
Ribo-lite reads were trimmed with cutadapt v1.14 with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to mouse/human rRNAs sequences (mm9/hg19) using Bowtie2 v2.2.2 with parameters --seedlen=23. Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of mm9/hg19 using STAR v2.5.3a with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. The gene expression level was then calculated by Cufflinks v2.2.1 based on the annotation of CDS region。
All mRNA-seq data were trimmed by Trim Galore v0.4.2 then mapped to transcriptome of mm9/hg19 by STAR v2.5.3a with parameters --outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was calculated by Cufflinks v2.2.1.
Genome_build: mm9

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/42 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

treatment_protocol: PN5 zygotes were obtained and cultured in KSOM containing either 0.1% DMSO or 60 μM DRB (Sigma; D1916). DRB was washed it away at the early 2-cell stage.

value: polyA RNA


title: KI-005


title: E3_DRB_L2C_smart

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/52 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

treatment_protocol: PN5 zygotes were obtained and cultured in KSOM containing either 0.1% DMSO or 60 μM DRB (Sigma; D1916). DRB was washed it away at the early 2-cell stage and embryos were continued to be cultured in KSOM till late 13-cell stage.

value: late 2-cell


title: O1_d9_SSEA4_Sendai_Exp1


title: E3_Ctr_L2C_Ribo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/44 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8557G).

treatment_protocol: PN5 zygotes were obtained and cultured in KSOM containing either 0.1% DMSO or 60 μM DRB (Sigma; D1916). DRB was washed it away at the early 2-cell stage and embryos were continued to be cultured in KSOM till late 5-cell stage.


title: KI-002


title: O1_d7_SSEA4_Sendai_Exp1


title: 70925-29

source_name: JI63-DAP35 kernel


title: 70925-27


title: KI-003

source_name: Glioma/GlioSarcoma

value: Glioma/GlioSarcoma


title: O1_Fib_Sendai_Exp2

source_name: Dermal fibroblast

value: Dermal fibroblast


title: 70925-33


title: KI-001


title: CD11c- CD11b+ MCs, 8 Gy radiotherapy, α-SIRPa, α-PD-1, E4

city: Houston

first: Michael

middle: A

last: Curran

state: TX

address: 1515 Holcombe Blvd.

department: Immunology

country: USA

institute: MD Anderson Cancer Center

data_processing:
KAPA RNA HyperPrep Kit with RiboErase (Roche Diagnostics; Indianapolis, IN) were utilized for library preparation. Sequencing-by-synthesis was performed on a HiSeq2500 utilizing v2 chemistry with paired-end 101-bp reads resulting in an average of 70.87 million paired-end reads per sample.
Sequence read data were processed and converted to FASTQ format for downstream analysis by Illumina BaseSpace analysis software, FASTQ Generation v1.0.0. Sequencing quality was examined using FastQC (Version 0.11.8), and adapter remnants, low quality bases, and short reads (< 20 nt) were trimmed.
The sequencing data were aligned to the mouse genome (grcm38) using HISAT2/StringTie/Ballgown as described by M Pertea et al. (Nat Protoc. 2016 Sep;11(9):1650-67.), and the read counts were extracted using a Python script (prepDE.py).
Normalized read counts and differential expression between experimental arms and untreated control were calculated using the edgeR package v3.34.0 in Bioconductor v3.12 in accordance with the User’s Guide (Y Chen et al. edgeR: differential analysis of sequence read count data).
Genome_build: grcm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Tumor-infiltrating CD11c- CD11b+ myeloid cells

extract_protocol:
Leukocytes in the irradiated tumors were harvested and dispersed into single-cell suspensions on day 17. CD11b-CD11c+, CD11b+CD11c+, and CD11b+CD11c- myeloid populations and CD8 T cells were isolated from the irradiated tumors using cell sorters, and RNA was extracted immediately after cell sorting. To increase the RNA yields and sample representativeness, we pooled the tumor-infiltrating leukocytes from 10 tumors (1 tumor per mouse) for each group.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MC38-OVA tumor-bearing mice were treated with or without 8-Gy focal radiotherapy (R; on day 12), αSIRPα (S; 400 μg on day 12, 14, and 16), and/or αPD-1 (P; 250 μg on day 12 and 15).

tag: strain

tag: treatment

value: 5 days after 8 Gy radiotherapy, anti-SIRPa, and anti-PD-1

tag: tumor cell line

value: MC38-OVA tumors


title: O1_d47_SSEA4_Sendai_Exp2


title: O1_d54_SSEA4_Sendai_Exp2

source_name: iPSC

value: iPSC


title: O1_d9_CD13_Sendai_Exp1

value: Failing to reprogram fibroblast


title: E3_Ctr_E2C_Ribo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/41 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8557G).

value: WT

value: early 2-cell

value: Ribosome protected fragment


title: mES_smart_rep2

source_name: Embryonic stem cell

growth_protocol: Mouse ES cells (R1) were cultured without irradiated mouse embryonic fibroblasts (MEFs) in DMEM containing 15% FBS, leukaemia inhibiting factor (LIF), penicillin/streptomycin, l-glutamine, β-mercaptoethanol, and non-essential amino acids.

extract_protocol: The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

value: Embryonic stem cell


title: 70925-26


title: mES_smart_rep1

growth_protocol: Mouse ES cells (R1) were cultured without irradiated mouse embryonic fibroblasts (MEFs) in DMEM containing 14% FBS, leukaemia inhibiting factor (LIF), penicillin/streptomycin, l-glutamine, β-mercaptoethanol, and non-essential amino acids.


title: O1_d40_SSEA4_Sendai_Exp2

value: Reprogramming fibroblast


title: CD11c+ CD11b- DCs, 8 Gy radiotherapy, α-SIRPa, α-PD-1, E3

source_name: Tumor-infiltrating CD11c+ CD11b- dendritic cells


title: O1_d7_CD13_Sendai_Exp1


title: O1_d34_SSEA4_Sendai_Exp2


title: 70925-25

source_name: JI63-DAP24 kernel


title: 70925-24


title: O1_d29_SSEA4_Sendai_Exp2


title: O1_d29_CD13_Sendai_Exp2


title: CD11c+ CD11b+ DCs, 8 Gy radiotherapy, α-PD-1, D2

source_name: Tumor-infiltrating CD11c+ CD11b+ dendritic cells

value: 5 days after 8 Gy radiotherapy and anti-PD-1


title: PN3_smart_rep2

source_name: Preimplantation embryo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/39 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

value: PN3 stage 1-cell


title: CD8 T cells, 8 Gy radiotherapy, α-SIRPa, α-PD-1, E1

source_name: Tumor-infiltrating CD8 T cells

value: Tumor-infiltrating CD8 T cells


title: CD11c- CD11b+ MCs, 8 Gy radiotherapy, α-PD-1, D4

value: Tumor-infiltrating CD11c- CD11b+ myeloid cells


title: 70925-22

value: kernel


title: O1_d21_SSEA4_Sendai_Exp2


title: 70925-14

source_name: DAN3130-DAP35 kernel


title: PN3_smart_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/36 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

value: polyA RNA


title: CD11c- CD11b+ MCs, 8 Gy radiotherapy, α-SIRPa, C4

value: 5 days after 8 Gy radiotherapy and anti-SIRPa


title: CD11c+ CD11b+ DCs, 8 Gy radiotherapy, α-SIRPa, α-PD-1, E2

value: Tumor-infiltrating CD11c+ CD11b+ dendritic cells


title: 70925-12


title: PN5_Ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/24 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8564G).

value: PN5 stage 1-cell


title: 70925-8

source_name: DAN3130-DAP24 kernel


title: mES_Ribo_rep1

extract_protocol: Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8566G).


title: mES_Ribo_rep2

extract_protocol: Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8567G).


title: O1_d21_CD13_Sendai_Exp2

source_name: Failing to reprogram fibroblast


title: 70925-11


title: 70925-13


title: CD11c+ CD11b+ DCs, 8 Gy radiotherapy, α-SIRPa, C2

value: MC38-OVA tumors


title: CD11c+ CD11b- DCs, 8 Gy radiotherapy, α-SIRPa, C3

value: Tumor-infiltrating CD11c+ CD11b- dendritic cells


title: CD8 T cells, 8 Gy radiotherapy, α-PD-1, D1


title: CD11c+ CD11b- DCs, 8 Gy radiotherapy, α-PD-1, D3


title: PN5_Ribo_rep2

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/25 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8565G).


title: O1_d15_CD13_Sendai_Exp1

value: Failing to reprogram fibroblast


title: 70925-10


title: O1_d15_SSEA4_Sendai_Exp1

source_name: Reprogramming fibroblast


title: MII_Ribo_rep2

source_name: Oocyte

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/19 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8559G).

value: WT

value: MII oocyte


title: PN3_Ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/22 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8562G).

value: Ribosome protected fragment


title: PN3_Ribo_rep2

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/23 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8563G).


title: O1_d13_SSEA4_Sendai_Exp1

extract_protocol:
RNA was extracted alongside the genomic DNA with the AllPrep DNA/RNA mini kit (Qiagen).
Libraries were prepared as previously described (Milagre et al, 2017), and run on a Hiseq 2500 (Illumina) for 75 bp paired-end sequencing.


title: CD11c- CD11b+ MCs, 8 Gy radiotherapy, B4

value: 5 days after 8 Gy radiotherapy


title: CD11c+ CD11b- DCs, 8 Gy radiotherapy, B3


title: CD8 T cells, 8 Gy radiotherapy, α-SIRPa, C1


title: O1_d11_SSEA4_Sendai_Exp2

value: Reprogramming fibroblast


title: Late2_Ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/16 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8556G).

value: late 2-cell


title: O1_d11_SSEA4_Sendai_Exp1


title: C6_day80_rep2

city: Ft Worth

first: Victor

last: Lin

address: 3500 Camp Bowie Blvd

institute: UNTHSC

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: RSN normalization in R

source_name: cerebral organoids, WA09 derived_CRISPR control (unedited, but went through editing process)

label_protocol: Standard Illumina label protocol

extract_protocol: RNA was extracted with Ambion MirVana Isolation Kit

tag: time point

tag: replicate

value: replicate 2


title: CD8 T cells, 8 Gy radiotherapy, B1

value: Tumor-infiltrating CD8 T cells


title: C6_day80_rep1

value: cerebral organoids, WA09 derived_CRISPR control (unedited, but went through editing process)

value: replicate 1


title: O1_d11_CD13_Sendai_Exp2


title: MII_Ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/18 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8558G).

tag: genotype

tag: developmental stage


title: Early2cell_Ribo_rep2

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/11 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8551G).

value: early 2-cell

tag: molecule


title: C6_day60_rep3

tag: cell type

value: replicate 3


title: ICM_Ribo_rep2

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/15 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8555G).

value: ICM


title: Late2_Ribo_rep2

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/17 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8557G).


title: O1_d13_CD13_Sendai_Exp1

tag: donor age

tag: days of reprogramming


title: CD11c+ CD11b+ DCs, 8 Gy radiotherapy, B2

extract_protocol:
Leukocytes in the irradiated tumors were harvested and dispersed into single-cell suspensions on day 17. CD11b-CD11c+, CD11b+CD11c+, and CD11b+CD11c- myeloid populations and CD8 T cells were isolated from the irradiated tumors using cell sorters, and RNA was extracted immediately after cell sorting. To increase the RNA yields and sample representativeness, we pooled the tumor-infiltrating leukocytes from 10 tumors (1 tumor per mouse) for each group.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tumor-infiltrating CD11c+ CD11b+ dendritic cells


title: CD11c+ CD11b- DCs, untreated, A3

value: untreated

value: MC38-OVA tumors


title: CD8 T cells, untreated, A1


title: Early2cell_50_Ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/10 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8550G).


title: N3_Fib_Sendai_Exp2

value: Dermal fibroblast


title: N3_d9_SSEA4_Sendai_Exp1


title: O1_d11_CD13_Sendai_Exp1

value: Failing to reprogram fibroblast


title: C6_day35_rep1


title: C6_day60_rep1


title: CD11c+ CD11b+ DCs, untreated, A2


title: 8cell_Ribo_rep2

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/9 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8549G).

value: WT


title: CD11c- CD11b+ MCs, untreated, A4

value: Tumor-infiltrating CD11c- CD11b+ myeloid cells


title: ICM_Ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/14 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8554G).

value: Ribosome protected fragment


title: N3_d9_CD13_Sendai_Exp1


title: 8cell_Ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/8 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8548G).


title: Hoxb8_input

city: Saint Louis

first: Tiantian

last: Liu

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

library_source: genomic

data_processing:
ChIP-seq reads were aligned and mapped to the mouse reference genome (GRCm38/mm10) by Bowtie software version 1.1.1: bowtie --sam --best -p 4 -t --verbose --trim5 5 -m 1 mm10 --chunkmbs 1000 Hoxb8_input.fastq > Hoxb8_input.sam; bowtie --sam --best -p 4 -t --verbose --trim5 5 -m 1 mm10 --chunkmbs 1000 Hoxb8_NFIL3_IP.fastq > Hoxb8_NFIL3_IP.sam
Duplicated reads are discarded using 'make tag directory' of Homer software package (version 4.9) with the parameter -tbp 1: makeTagDirectory Hoxb8_input.tags Hoxb8_input.sam -tbp 1; makeTagDirectory Hoxb8_NFIL3_IP.tags Hoxb8_NFIL3_IP.sam -tbp 1
Data were visualized with the 'makeUCSCfile' of Homer: makeUCSCfile Hoxb8_input.tags -o Hoxb8_input.bedgraph -fsize 5e7 -res 1; makeUCSCfile Hoxb8_NFIL3_IP.tags -o Hoxb8_NFIL3_IP.bedgraph -fsize 5e7 -res 1
Peak calling and de novo motif discovery were performed with Homer software package.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated with Homer software package using the "makeUCSCfile" command.

molecule: genomic DNA

source_name: bone marrow progenitor cells

growth_protocol: BM cells were isolated from 6 week old mice and CD3-, CD19-, CD105-, TER-119-, Ly-6G- and B220-expressing lineage-committed cells were depleted. The lineage– BM cells were cultured in complete IMDM supplemented with 50 ng/ml SCF (Peprotech), 25 ng/ml IL-3 (Peprotech), 25 ng/ml IL-6 (Peprotech), and 5% Flt3L-conditioned medium for 2 days and then retrovirally transduced with MSCV-Neo-FLAG-ER-Hoxb8. Three days after infection, 1 mM β-estradiol (Sigma Aldrich) and 1 mg/ml G418 were added to select and maintain growth of ER-Hoxb8-transduced cells.

extract_protocol:
Thirty million cells were crosslinked with 1% formaldehyde for 5 min, quenched with 1/20 volume of 2.5 M glycine and washed twice with PBS. To obtain nuclei, cell pellets were incubated in 1 mL Lysis buffer 1 (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40 and 0.25% Triton X-100) supplemented with protease inhibitors for 10 min, and 1 mL Lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) supplemented with protease inhibitors for 10 min. To shear chromatin, nuclei pellets were gently rinsed with Shearing buffer D3 (10 mM Tris-HCl, pH 7.6, 1 mM EDTA, and 0.1% SDS) twice, and then sonicated at 4 °C in Shearing buffer D3 for 17 min, of 10% duty cycle, 75 Watts intensity peak incident power and 200 cycles per burst, with an ME220 focused-ultrasonicator (Covaris). A 5% fraction of lysate were kept for input, and the remaining lysate were immunoprecipitated overnight at 4 °C with Dynabeads Protein G (Invitrogen) that had been pre-incubated with 5 mg of goat anti-NFIL3 antibody (sc-9550X; Santa Cruz Biotechnology). Beads containing protein-DNA complexes were washed and DNA fragments were reverse-crosslinked and eluted.
Libraries were prepared with a ThruPLEX DNA-seq kit (Rubicon Genomics) and cleaned-up with AMPureXP.

treatment_protocol: The Hoxb8 cell line stably expressing Flag-NFIL3 was generated by retrovirally transducing with MSCV-Flag-NFIL3-IRES-GFP vector and sorting for expression of GFP.

tag: cell line

value: Hoxb8 hematopoietic progenitor cell line stably expressing Flag-NFIL3

tag: chip antibody


title: N3_d7_SSEA4_Sendai_Exp1

value: Reprogramming fibroblast


title: Hoxb8_NFIL3_IP

value: NFIL3 (Santa Cruz Biotechnology, sc-9550X, Lot# G0815)


title: N3_d7_CD13_Sendai_Exp1


title: 4cell_Ribo_rep2

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/7 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8547G).


title: bts-1

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences using Cutadapt v1.12, and then aligned to the Arabidopsis thaliana reference genome (TAIR10) using TopHat v2.1.0 with parameters -r 100 --library-type fr-firststrand --mate-std-dev 100 -p 24 --bowtie-n.
After the alignment, the number of reads mapped to gene features were counted using HTSeq v0.9.1.
Fragments per kilobase of transcript per million fragments mapped (FPKM) was calculated by dividing the mapped read counts by gene length and total number of reads mapped onto protein-coding genes. The ‘expressed’ genes were first identified as the ones with FPKM larger than 1 in at least one sample. For these expressed genes, FPKM values were converted to log2-FPKM values after adding one to the FPKM values. The log2-FPKM values for the samples were then normalized using the quantile normalization method (MATLAB R2021a).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files including normalized log2-FPKM values for each sample

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings of bts-1 mutant

extract_protocol:
Total RNAs were prepared from Arabidopsis shoot tissues at the following two conditions: wild-type (Col-0) and bts-1 mutant (bts-1) grown on 1/2 MS medium without sucrose. Total RNA was isolated from shoot tissues using the Qiagen RNeasy mini kit according to the manufacturer's instructions. RNA was treated with TURBO DNase (Invitrogen).
Libraries were prepared for multiplex sequencing using a NEXTflex Rapid Directional RNA-seq Kit (Perkin Elmer), following the manufacturer’s instructions.

tag: tissue

value: shoot

value: bts-1 mutant


title: C6_day60_rep2

value: cerebral organoids, WA09 derived_CRISPR control (unedited, but went through editing process)

value: replicate 2


title: GFP+_BM

data_processing:
Library strategy: CUT&RUN
The adaptor sequences were removed by Trimmomatic program: java -jar trimmomatic-0.39.jar PE -threads 30 -phred33 WT_CEBPa_R1.fastq.gz WT_CEBPa_R2.fastq.gz -baseout WT_CEBPa.fastq.gz ILLUMINACLIP:Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25
The trimmed reads were aligned and mapped to the mouse reference genome (GRCm38/mm10) by Bowtie2 software version 2.2.5: bowtie2 -p 30 --dovetail --phred33 -x mm10 -1 WT_CEBPa_1P.fastq.gz -2 WT_CEBPa_2P.fastq.gz > WT_CEBPa.sam
Duplicated reads are discarded using 'make tag directory' of Homer software package (version 4.9) with the parameter -tbp 1: makeTagDirectory WT_CEBPa.tags WT_CEBPa.sam -fragLength given -tbp 1
Data were visualized with the 'makeUCSCfile' of Homer: makeUCSCfile WT_CEBPa.tags -o auto -fragLength given -tbp 1 -fsize 5e7
Peak calling was performed with Homer software package: findPeaks WT_CEBPa -style factor -size 200 -o WT_CEBPa.txt -i negative_control -poisson 1e-10
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated with Homer software package using the "makeUCSCfile" command.

growth_protocol: BM cells were isolated from Nfil3GFP/GFP mice and CD3-, CD19-, B220-, CD105-, TER-119-, Ly-6G-, CD4-, CD8b-, CD11b-, Ly-6C- and MHCII-expressing lineage-committed cells were depleted. GFP-NFIL3 negative BM and GFP-NFIL3 positive BM cells were sort purified.

extract_protocol:
0.7 million fresh sort purified cells were adsorbed to activated Concanavalin A (ConA) beads, permeabilized with 0.01% digitonin, and incubated with 0.5 mg goat-anti-NFIL3 antibody overnight at 4 °C. After antibody binding, the targete-DNA complex is cleaved by the Protein A/Protein G-Micrococcal Nuclease (pAG-MNase) for 2 hours at 4 °C. 0.05ng E. coli Spike-in DNA was added before releasing CUT&RUN fragments at 37°C for 10 min. The CUT&RUN enriched DNA is purified from the supernatant.
Libraries were prepared with a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and cleaned-up with AMPureXP.

treatment_protocol: Nfil3GFP/GFP mice were injected once daily, subcutaneously, with 10 mg recombinant Flt-3L-Ig (BE0098; Bio X Cell) for three consecutive days to expand GFP-NFIL3+ DC progenitor cell numbers.

value: GFP-NFIL3 positive BM

tag: chip or cut&run antibody


title: 4cell_Ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/6 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8546G).


title: C6_day21_rep1

value: replicate 1


title: C6_day35_rep2


title: C6_day21_rep2


title: C6_day14_rep2


title: N3_d54_SSEA4_Sendai_Exp2

extract_protocol:
RNA was extracted alongside the genomic DNA with the AllPrep DNA/RNA mini kit (Qiagen).
Libraries were prepared as previously described (Milagre et al, 2017), and run on a Hiseq 2500 (Illumina) for 75 bp paired-end sequencing.

value: iPSC


title: C6_day14_rep1


title: Cystic Fibrosis 3 Protein

city: Lebanon

first: Claudia

middle: V

last: Jakubzick

state: NH

address: 1 Medical Center Drive, Rm 626 W Borwell, PO#1250960

department: Microbiology and Immunology

institute: Dartmouth College

description:
Protein
CD88, CD1c, CD1a, CD64, CD14, CD93, CD197, XCR1, CD163, CD36, CD206, HLA-DR, CD169 TotalSeq B (BioLegend, San Diego, CA) were incubated for 30 min on ice

data_processing:
Data Preparation:  Raw sequencing reads were demultiplexed, mapped to the GRCh38 human reference genome, and gene-expression matrices were generated using CellRanger v6.1 (10X Genomics, Pleasanton, CA). The following analyses were conducted in R 4.1 (23) and Python 3.6. Seurat package v4.0 was used for downstream data analyses (24) and figures were produced using the package ggplot2. Following a standard workflow, the gene-expression matrix was filtered to discard cells with less than 200 genes, as well as genes that were expressed in less than 3 cells. Samples then went through quality control to remove cells with either too many or too few expressed genes (average around 2000 and 7000) and cells with too many mtRNA (average around 10%), resulting in a total of 113,213 cells. Then, "SCTransform" was applied with the "glmGamPoi" method to normalize gene expression data (25, 26), and a CLR transformation was applied to normalize protein data within each cell. After individual preparation, all the samples were introduced into a combined Seurat object via “FindIntegrationAnchors” and “IntegrateData” functions (25). Then scaled values of variable genes were then subject to principal component analysis (PCA) for linear dimension reduction. A shared nearest neighbor network was created based on Euclidean distances between cells in multidimensional PC space (the first 50 PC were used) and a fixed number of neighbors per cell (30 neighbors). This was used to generate a two-dimensional Uniform Manifold Approximation and Projection (UMAP) for visualization as a harmonized atlas to dissect the cell populations in BALF of healthy and CF donors.
TotalSeq antibodies: TotalSeq antibodies were added at concentrations recommended by the manufacturer and stained for 30 min on ice (1). CD88 (B1046), CD1c (B0160), CD1a (B0402), CD64 (B0162), CD14 (B0081), CD93 (B0446), CD197 (B0148), XCR1 (B0208), CD163 (B0358), CD36 (B0407), CD206 (B0205) HLA-DR (B0159), CD169 (B0206) TotalSeq B (BioLegend, San Diego, CA).  TotalSeq antibodies were added to the last four samples (HC3, HC4, CF2, CF3).
Differentially Expressed Genes: Differentially expressed genes (DEGs) were calculated with "FindAllMarkers" function of Seurat in R 4.1 to study the different expression profiles in different cell types and up-regulated genes in HC or CF cohort (2, 3). The "data" matrices of "SCT" assay were used, and the minimal log fold change was set to 0.25. Only genes that were detected in more than 25% of cells in either of the two populations were used to compute the DEGs with the Wilcoxon rank-sum test. Markers were identified as genes exhibiting significant upregulation when compared against all other clusters and defined by having a Bonferroni adjusted p-value < 0.05. The DEGs are ranked by the adjusted p--value to select the top DEGs for downstream analysis.
Cell type Identification: To identify cell types, "FindClusters" function with the Leiden algorithm with the various resolution from 0.5 to 2.0 in the Seurat package were used for clustering (3). "FindAllMarkers" function was then applied. The top DEGs of individual clusters were examined for well-studied marker genes across literatures and the clusters were then annotated for the most likely identity. For re-clustered AMs and Mono subtypes, "FindClusters" was performed with different resolution until the right resolution is reached so that each cluster has unique gene expression pattern.
Genome_build: GRCh38
Supplementary_files_format_and_content: Integrated SeuratObject in rds format containing all 7 samples and different assays of expression/detection matrixes (for both mRNA and protein); The meta data in txt format for every cells, including the sample source, cell types, and UMAP coordinates (for both overall UMAP and reclustered AMs UMAP)

source_name: BALF

extract_protocol:
Four healthy control (HC) subjects and three subjects with CF underwent research bronchoscopy as previously described (20, 21). Briefly, after local anesthesia to the posterior pharynx and intravenous conscious sedation, a flexible fiberoptic bronchoscope was inserted transorally and passed through the vocal cords into the trachea. The bronchoscope was sequentially wedged into tertiary bronchi in the right upper lobe (RUL), right middle lobe (RML) and right lower lobe (RLL), saline was instilled, and BALF was collected. An aliquot of 10 mL of BALF from the RML was used for the studies outlined here. All subjects provided written informed consent, and this study was approved by the Institutional Review Board of Dartmouth-Hitchcock Medical Center (protocol #22781). Sample processing and library construction were performed immediately after lavage. 1X phosphate-buffered saline (PBS) containing 0.5 mM EDTA, and 0.1% bovine serum albumin (BSA) was added to the BALF. Samples were filtered through 100-micron cell strainers and centrifugated at 300 x g for five minutes at 4 °C and supernatants were discarded. TotalSeq antibodies were added at concentrations recommended by the manufacturer and stained for 30 min on ice (22), details in online supplement. After staining, chilled Hank's balanced salt solution (HBSS) supplemented with 0.5% BSA was used to wash the sample. Samples were again filtered through 100-micron cell strainers and spun as above. Supernatants were aspirated, and pellets were resuspended with HBSS plus 0.5% BSA at an approximate concentration of 7.5 × 105 cells/mL.
Cell quality and viability of the samples were assessed with a Cellometer K2 (Nexcellom Bioscience). All samples had viability >80%. Single cells were then processed using the Chromium Next GEM Single Cell 3' Platform (10X Genomics, Pleasanton, CA). Approximately 30,000 cells were loaded on each channel with an average recovery rate of 24,000 cells. Libraries were sequenced on NextSeq 500/550 with an average sequencing depth of 50,000 reads/cell (Illumina, San Diego, CA).

tag: disease

value: Cystic Fibrosis


title: N3_d47_SSEA4_Sendai_Exp2


title: GFP-_BM

value: GFP-NFIL3 negative BM


title: Cystic Fibrosis 3 mRNA


title: N3_d34_SSEA4_Sendai_Exp2


title: N3_d40_SSEA4_Sendai_Exp2


title: Cystic Fibrosis 2 Protein


title: Control heart tissues for H3K4me3 CUT&Tag at P17

city: Nanjing

first: Yingchao

last: Shi

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

data_processing:
Library strategy: CUT&Tag
Sequencing reads were aligned to the mouse mm10 reference genome with Bowtie2 (v2.4.4). Duplicated reads were removed with sambamba markdup (v0.8.1). MACS2 was used to call peaks.
Peaks were called using macs2 callpeak with the following setting: -g mm -p 0.005 -f AUTO --nomodel --shift -100 --extsize 200 --keep-dup all --call-summits -B --SPMR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_peak.txt: Peak text files.

source_name: heart

extract_protocol:
Fresh mouse heart tissues (atrial tissues were removed) were used for extracting nuclei with nuclear extraction kit (Solarbio, SN0020). CUT&Tag assays were performed using the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (Vazyme, TD902-02).
Libraries were prepared using Vazyme's instructions accompanying the kits (Vazyme, TD902-02, TD202).

value: Heart

value: Znhit1 flox/flox

tag: age

value: postnatal day 17

tag: antibody

value: H3K4me3 (Abcam, ab1012)


title: Col-0

source_name: Arabidopsis seedlings of wild-type (Col-0)

value: wild-type (Col-0)


title: C6_day6_rep1

extract_protocol: RNA was extracted with Ambion MirVana Isolation Kit


title: Znhit1-cKO heart tissues for H3K27me3 CUT&Tag at P17

tag: strain

value: Znhit1 flox/flox;Myh6-Cre


title: N3_d29_SSEA4_Sendai_Exp2

value: Reprogramming fibroblast


title: C6_day0_rep2


title: C6_day0_rep1


title: C6_day6_rep2


title: Cystic Fibrosis 2 mRNA


title: N3_d29_CD13_Sendai_Exp2

value: Failing to reprogram fibroblast


title: Znhit1-cKO heart tissues for H3K4me3 CUT&Tag at P17


title: C4_day80_rep1

source_name: cerebral organoids, WA09 derived_NGLY1 KO clone 4


title: Cystic Fibrosis 1 Protein

description:
Protein
CD88, CD1c, CD1a, CD64, CD14, CD93, CD197, XCR1, CD163, CD36, CD206 TotalSeq B (BioLegend, San Diego, CA) were incubated for 30 min on ice


title: Control heart tissues for H3K27me3 CUT&Tag at P17


title: Znhit1-cKO heart tissues for H2A.Z CUT&Tag at P17


title: N3_d21_SSEA4_Sendai_Exp2


title: C4_day80_rep2

value: cerebral organoids, WA09 derived_NGLY1 KO clone 4


title: Cystic Fibrosis 1 mRNA


title: N3_d21_CD13_Sendai_Exp2


title: Healthy Control 4 mRNA

value: Healthy


title: C4_day35_rep1


title: Healthy Control 4 Protein


title: N3_d15_CD13_Sendai_Exp1


title: Control heart tissues for H2A.Z CUT&Tag at P17


title: Znhit1-cKO heart tissues for H2A.Z CUT&Tag at P25

value: postnatal day 25


title: C4_day35_rep2

value: replicate 2


title: N3_d13_SSEA4_Sendai_Exp1


title: C4_day21_rep2


title: N3_d13_CD13_Sendai_Exp1


title: Healthy Control 3 Protein


title: Healthy Control 3 mRNA


title: Control heart tissues for H2A.Z CUT&Tag at P25_rep1


title: Healthy Control 2 Protein


title: C4_day14_rep1


title: C4_day21_rep1


title: C4_day14_rep2


title: N3_d15_SSEA4_Sendai_Exp1


title: N3_d11_SSEA4_Sendai_Exp2


title: Znhit1 cKO heart tissues at P25_rep3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR (V2.7.1a) with default parameters.
Fragments per kilobase per million reads (FPKM) were calculated using cuffnorm (v2.2.1) with default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: *_RNA_seq_FPKM_matrix.txt: Tab-delimited text files include FPKM value matrix at P17 and P25.

extract_protocol:
Mouse hearts (atrial tissues were removed) were snap-frozen and stored at -80℃ until use. Total RNA was isolated using TRIzol regents.
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.

value: heart


title: Healthy Control 2 mRNA


title: Control heart tissues for H2A.Z CUT&Tag at P25_rep2


title: Znhit1 cKO heart tissues at P25_rep2


title: N3_d11_CD13_Sendai_Exp2


title: Control heart tissues at P25_rep2


title: Znhit1 cKO heart tissues at P25_rep1


title: N3_d11_CD13_Sendai_Exp1


title: Healthy Control 1 Protein


title: Healthy Control 1 mRNA


title: N2_Fib_Sendai_Exp2

source_name: Dermal fibroblast

value: Dermal fibroblast


title: C4_day6_rep2


title: 54 (WAS-C)

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description:
WTmac_vs_WASC_gene_exp.diff
WTmac_vs_WASC_isoform_exp.diff

data_processing:
FastQC v0.11.5 with default parameter was used for quality test.
RNA-Seq reads were mapped to hg19 reference genome by STAR v2.5.1 with default parameters. RNA-Seq gene expression (RNA-Seq_fpkm_WAS.txt) was performed by Homer that reads uniquely mapped to the exon region of each RefSeq gene were counted and normalized into FPKM value. Gene and isoform level differential expression analysis was performed by cuffdiff v2.2.1 with parameter -b -u --library-type fr-firststrand.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file for RNA-Seq analysis

molecule: polyA RNA

source_name: WAS-C

growth_protocol: Human fibroblasts from a Wiskott-Aldrich syndrome patient with the c.1271dupG mutation (in the WAS gene were purchased from the Coriell institute (Camden, NJ). Human fibroblasts from a Wiskott-Aldrich syndrome patient with the c.107_108del mutation and from the mother of the patient (unaffected) were purchased from the Cell Line and DNA Bank from Patients Affected by Genetic Diseases (Genova, Italy). The B-lymphocyte cell lines ID00003 (WAS: c.431G>A) and GM11518 (wild type) were purchase from the Coriell institute (Camden, NJ). iPSCs cultured on MEF feeders in human ESC medium were manually dissociated and plated on 8 days old overgrown OP9 feeders to start differentiation. Cells were co-cultured with the OP9 feeders for 12-14 days in OP9 differentiation medium (Alpha MEM containing 10% FBS, 100 μM monothioglycerol and 50 μg/ml ascorbic acid) as described by Vodyanik, M. A. & Slukvin, II. (Curr Protoc Cell Biol 2007). Differentiated cells were dissociated with collagenase and Accutase (Innovative Cell Technologies) and subjected to further differentiation into macrophages using GM-CSF and M-CSF. Human B cells, T cells and monocytes were sorted on a FACSAria II cell sorter using CD19, CD4 and CD14 antibodies, respectively. Macrophages were derived from PBMCs monocyte in the presence of M-CSF.

extract_protocol:
RNA was isolated by Qiagen RNeasy micro kit with in column DNase digestion.
The Agilent TapeStation or Bioanalyzer was used to determine RNA integrity (RIN) numbers prior to library preparation. Stranded mRNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina). Briefly, RNA with polyA tail was isolated using poly-T oligos conjugated to magnetic beads. mRNA was then fragmented and reverse-transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. dUTP-incorporated second strand was not amplified. cDNA was then end-repaired, index adapter-ligated and PCR amplified. Purification of nucleic acids after each enzymatic steps was achieved by using AMPure XP beads (Beckman Coulter).

value: WAS-C

value: macrophage


title: N2_d9_SSEA4_Sendai_Exp1


title: 53 (WAS-C)


title: 52 (WT)

source_name: WT-2 MAC

value: WT


title: Control heart tissues at P25_rep3


title: N3_d11_SSEA4_Sendai_Exp1


title: Znhit1 cKO heart tissues at P17_rep2


title: Znhit1 cKO heart tissues at P17_rep3


title: N2_d9_CD13_Sendai_Exp1


title: Control heart tissues at P25_rep1


title: Znhit1 cKO heart tissues at P17_rep1


title: N2_d7_SSEA4_Sendai_Exp1


title: Control heart tissues at P17_rep3


title: C4_day0_rep1

value: replicate 1


title: C4_day0_rep2


title: C4_day6_rep1


title: 49 (WT)

source_name: WT-1 MAC


title: 47 (WT)

description:
WTB_vs_WASB_gene_exp.diff
WTB_vs_WASB_isoform_exp.diff

source_name: WT-1 B

value: B cell


title: C3_day80_rep1

source_name: cerebral organoids, WA09 derived_NGLY1 KO clone 3


title: C3_day80_rep2

value: cerebral organoids, WA09 derived_NGLY1 KO clone 3


title: C3_day60_rep1


title: 50 (WT)

source_name: WT-2 B


title: N2_d54_SSEA4_Sendai_Exp2

source_name: iPSC

value: iPSC


title: C3_day35_rep2


title: C3_day60_rep3

value: replicate 3


title: Control heart tissues at P17_rep2

value: Znhit1 flox/flox

value: postnatal day 17


title: C3_day60_rep2


title: 43 (WAS P2)

source_name: WAS P2 B

value: WAS P2


title: N2_d7_CD13_Sendai_Exp1

source_name: Failing to reprogram fibroblast

value: Failing to reprogram fibroblast


title: N2_d34_SSEA4_Sendai_Exp2

source_name: Reprogramming fibroblast

value: Reprogramming fibroblast


title: Control heart tissues at P17_rep1


title: N2_d47_SSEA4_Sendai_Exp2


title: B cell Nfil3-KO rep2

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Genome_build: Mouse Ensembl GRCm38.76 (mm10)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with merged differential expression results

source_name: spleen B cell

growth_protocol: CD317- B220- MHC II+ CD11c+ XCR1+ CD172a- cDC1s were sorted from CD11c enriched splenocytes. CD19+ B220+ B cells were sorted from splenocytes.

extract_protocol:
RNA was isolated from 200,000 live B cells sorted after stimulation or 120,000 cDC1 using NucleoSpin RNA XS Kit (Macherey-Nagel).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: B cells were stimulated with IL-4 (20 ng/mL) and LPS (5 mg/mL) for 24 hours.

value: spleen

tag: treatment

value: IL-4 (20ng/mL) + LPS (5ug/mL) for 24 hours


title: N2_d40_SSEA4_Sendai_Exp2


title: 41 (WAS P1)

source_name: WAS P1 B

value: WAS P1


title: C3_day35_rep1

tag: time point


title: 58 (WAS-B corrected)

description:
WASBcor_vs_WASBun_gene_exp.diff
WASBcor_vs_WASBun_isoform_exp.diff

source_name: hu-iPSC-macrophage-RNA, corrected WAS-B

value: WAS-B corrected


title: C3_day14_rep2

tag: replicate

value: replicate 2


title: C3_day21_rep1


title: 64 (WAS-B)

source_name: hu-iPSC-macrophage-RNA, WAS-B

tag: genotype

value: WAS-B

value: macrophage


title: 48 (WT)

description:
WTT_vs_WAST_gene_exp.diff
WTT_vs_WAST_isoform_exp.diff

source_name: WT-1 T

value: WT

value: T cell


title: 44 (WAS P2)

source_name: WAS P2 T


title: N2_d29_SSEA4_Sendai_Exp2


title: N2_d21_SSEA4_Sendai_Exp2


title: N2_d29_CD13_Sendai_Exp2


title: C3_day21_rep2

value: cerebral organoids, WA09 derived_NGLY1 KO clone 3


title: C3_day14_rep1

value: replicate 1


title: 51 (WT)

source_name: WT-2 T


title: B cell GFP-NFIL3 rep1

value: B cell


title: B cell Nfil3-KO rep1


title: B cell WT rep2

value: wild type


title: B cell WT rep1


title: ML4 (WAS-B)

description:
WASBcor_vs_WASBun_gene_exp.diff
WASBcor_vs_WASBun_isoform_exp.diff
RNA-seq_fpkm_WAS.txt


title: B cell GFP-NFIL3 rep2


title: N2_d15_CD13_Sendai_Exp1


title: 42 (WAS P1)

source_name: WAS P1 T


title: C3_day6_rep1


title: N2_d15_SSEA4_Sendai_Exp1


title: C3_day6_rep2


title: cDC1 WT rep2

source_name: spleen cDC1


title: ML3 (WT)

source_name: hu-CB-macrophage-RNA, WT-cb


title: N2_d13_CD13_Sendai_Exp1


title: ML2 (WAS-C corrected)

source_name: hu-iPSC-macrophage-RNA, corrected WAS-C

value: WAS-C corrected


title: N2_d21_CD13_Sendai_Exp2


title: cDC1 WT rep1


title: N2_d13_SSEA4_Sendai_Exp1


title: ML15 (WAS-B corrected)

source_name: hu-iPSC-macrophage, corrected-WAS-B


title: H9_day80_rep2

source_name: cerebral organoids, WA09 derived_parent (unedited, did not undergo CRISPR editing)


title: N2_d11_SSEA4_Sendai_Exp2


title: cDC1 GFP-NFIL3 rep1


title: cDC1 GFP-NFIL3 rep2


title: ML1 (WAS-C)

source_name: hu-iPSC-macrophage-RNA, WAS-C

value: WAS-C


title: ML5 (WAS-B corrected)


title: WT_NFIL3

data_processing:
The adaptor sequences were removed by Trimmomatic program: java -jar trimmomatic-0.39.jar PE -threads 30 -phred33 WT_CEBPa_R1.fastq.gz WT_CEBPa_R2.fastq.gz -baseout WT_CEBPa.fastq.gz ILLUMINACLIP:Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25
The trimmed reads were aligned and mapped to the mouse reference genome (GRCm38/mm10) by Bowtie2 software version 2.2.5: bowtie2 -p 30 --dovetail --phred33 -x mm10 -1 WT_CEBPa_1P.fastq.gz -2 WT_CEBPa_2P.fastq.gz > WT_CEBPa.sam
Duplicated reads are discarded using 'make tag directory' of Homer software package (version 4.9) with the parameter -tbp 1: makeTagDirectory WT_CEBPa.tags WT_CEBPa.sam -fragLength given -tbp 1
Data were visualized with the 'makeUCSCfile' of Homer: makeUCSCfile WT_CEBPa.tags -o auto -fragLength given -tbp 1 -fsize 5e7
Peak calling was performed with Homer software package: findPeaks WT_CEBPa -style factor -size 200 -o WT_CEBPa.txt -i negative_control -poisson 1e-10
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated with Homer software package using the "makeUCSCfile" command.

source_name: bone marrow progenitor cells

growth_protocol: BM cells were isolated from 6 week old WT or D1+2+3 mice and CD3-, CD19-, CD105-, TER-119-, Ly-6G- and B220-expressing lineage-committed cells were depleted. The lineage– BM cells were cultured in complete IMDM supplemented with 50 ng/ml SCF (Peprotech), 25 ng/ml IL-3 (Peprotech), 25 ng/ml IL-6 (Peprotech), and 5% Flt3L-conditioned medium for 2 days and then retrovirally transduced with MSCV-Neo-ER-Hoxb8. Three days after infection, 1 mM β-estradiol (Sigma Aldrich) and 1 mg/ml G418 were added to select and maintain growth of ER-Hoxb8-transduced cells.

extract_protocol:
0.5 million fresh cells were adsorbed to activated Concanavalin A (ConA) beads, permeabilized with 0.01% digitonin, and incubated with 0.5 mg indicated antibodies overnight at 4 °C. After antibody binding, the targete-DNA complex is cleaved by the Protein A/Protein G-Micrococcal Nuclease (pAG-MNase) for 2 hours at 4 °C. 0.05ng E. coli Spike-in DNA was added before releasing CUT&RUN fragments at 37°C for 10 min. The CUT&RUN enriched DNA is purified from the supernatant.
Libraries were prepared with a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and cleaned-up with AMPureXP.
OTHER: CUT&RUN

treatment_protocol: The Hoxb8 cell lines stably expressing Flag-NFIL3 or C/EBPa were generated by retrovirally transducing with MSCV-Flag-NFIL3-IRES-GFP or MSCV-C/EBPa-T2A-Thy1.1 vectors and sorting for expression of GFP or Thy1.1.

value: Hoxb8 hematopoietic progenitor cell line stably express Flag-NFIL3

value: FLAG (Sigma, F1804, clone M2)


title: H9_day35_rep1

value: cerebral organoids, WA09 derived_parent (unedited, did not undergo CRISPR editing)


title: N2_d11_CD13_Sendai_Exp2

source_name: Failing to reprogram fibroblast

value: Failing to reprogram fibroblast


title: H9_day35_rep2


title: N2_d11_SSEA4_Sendai_Exp1

source_name: Reprogramming fibroblast

value: Reprogramming fibroblast


title: D1+2+3_NFIL3


title: C3_day0_rep1

source_name: cerebral organoids, WA09 derived_NGLY1 KO clone 3


title: WT_C/EBPb

value: Hoxb8 hematopoietic progenitor cell line

value: C/EBPb (Santa Cruz Biotechnology, sc-7962X, Lot# D2821)


title: D1+2+3_C/EBPa

value: Hoxb8 hematopoietic progenitor cell line stably express C/EBPa

value: C/EBPa (Cell Signaling Technology, 8178S, Lot3)


title: H9_day14_rep2

value: replicate 2


title: C3_day0_rep2


title: H9_day21_rep1


title: H9_day80_rep1


title: N2_d11_CD13_Sendai_Exp1


title: D1+2+3_C/EBPb


title: WT_C/EBPa


title: Sample 21: P2.T.P.1

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
The quality of the data was assessed using FastQC, MultiQC, PCAs, Jaccard Similarity Indices and MA plots
the reads were aligned using STAR v2.7.3a (parameters --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --readFilesCommand gunzip -c)
Protein-coding gene quantification was performed using Subread featureCounts v2.0.0 (default parameters)
The raw expression levels were normalized with edgeR v3.26.8. After normalization, a noise filtering step was applied i.e. for each gene, if the maximum normalised expression level was <10 then the gene was excluded from the downstream analysis.
Statistical testing for differential expression of genes was performed using edgeR, with multiple-testing correction based on the Benjamini-Hochberg method. DE Genes were called on adj p-value < 0.05, and |log2(FC)| > 0.5.
The enrichment analysis was performed using g:profiler (Reimand et al., Nucleic Acids Research, 2016)
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: raw.csv contains raw gene counts; normalized.csv contains edgeR-normalized expression levels after the application of the noise filter

source_name: Primary CLL cells

growth_protocol: Primary CLL cells were transfected with NSC or ZAP-70 siRNA and co-cultured with EL08 stromal cells in RPMI 1640 medium for totally 7 days.

extract_protocol:
Primary CLL cells were harvested after positivley selected by anti-CD19 beads and total RNA was extracted using the standard protocol from GenElute Mammalian Total RNA Miniprep Kit (Sigma/RTN70).
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB #7420) was used with 100ng of total RNA for the construction of sequencing libraries. mRNA was isolated and purified by using NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #7490) before cDNA synthesis.

treatment_protocol: For samples with anti-IgM treatment, primary CLL cells were co-cultured with EL08 stromal cells and treat with anti-IgM 4ug/1x10^6 CLL cells.

tag: patient

tag: disease state

value: Chronic Lymphocytic Leukemia

value: Rep 1


title: H9_day6_rep2

tag: cell type


title: Sample 18: P2.C.P.3

value: NSC

value: Rep 3


title: Sample 23: P2.T.P.3


title: H9_day21_rep2


title: Sample 17: P2.C.P.2

value: Rep 2


title: negative_control

value: Rabbit IgG


title: SW1353_RRBS_rep3_G30

city: Shanghai

first: Jianing

last: Wang

address: Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
RRBS reads were trimmed using Trim Galore, reads containing adapter were discarded.
Then used Bismark to align trimmed reads to hg38 genome
Next Bismark comes with a supplementarybismark_methylation_extractor script which operates on Bismark result files and extracts the methylation call for every single C analyzed.
Then we merged all the triplicate data to classify 100% ,50% and 0% methylation sites
Assembly: hg38 (GRCh38)
Supplementary files format and content: Tab-delimited text file includes chromosome position and methylation level for each 100%,50%,0% methylation fidelity CpG site .

source_name: chondrosarcoma

growth_protocol: The cells were cultured with DMEM/F-12 medium (Biological Industries, Israel) containing 20% fetal bovine serum (Gibco BRL/Invitrogen, Carlsbad, CA, USA), 100μg/ml streptomycin, and 100IU/ml penicillin, and incubated with 37℃ and 5% CO2.

extract_protocol:
Genomic DNA from ARPE-19,Jurkat and SW1353 was extracted by using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.Two microgram of genomic DNA was used to construct the RRBS library by NEBNext Ultra II library kit and EZ DNA Methylation-Gold™ Kit (Zymo Research) following the manufacturer’s protocol. The quality of libraries was assessed with Agilent 2100 Bioanalyzer (Agilent, United States).
To evaluate the conversion error of bisulfite conversion, the methylated spike in and unmethylated spike in were used. We chose two different regions as the templates from the λDNA. One template was amplified with dNTP Mix to synthesize the unmethylated spike in, and the other one was amplified with 5-Methylcytosine dNTP Mix to synthesize the methylated spike in. Then the spike in were fragmented to about 300bp by Covaris (Covaris, USA). After constructing libraries using NEBNext Ultra II Library Prep Kit for Illumina® separately, the methylated spike in and unmethylated spike in were mixed together and spiked to the DNA at a ratio of 1% before bisulfite conversion. Two micrograms of genomic DNA were used for MspI (NEB, San Diego, California, USA) digestion. And the fragments were recovery by using AxyPrep PCR Clean kit. After constructing the sequencing library and mixing the spike in, bisulfite conversion was performed on the libraries by the EZ DNA Methylation-Gold Kit (Zymo Research, USA), which was also used to recovery the libraries. Epimark Hot Start Enzyme was used for PCR to amplify the libraries. To obtain the fragments exactly, the vertical TBE-PAGE electrophoresis was performed on the 6% TBE-PAGE Gel (Novex, Invitrogen, USA) to better separate the bands. After recovering the libraries from the gel, the Agilent 2100 Bioanalyzer system (Agilent, USA) was used for assessing the distribution of libraries.

treatment_protocol: Serum starvation for 24h before collecting the sample.

value: chondrosarcoma

value: Fibroblast Cells

value: Normal culture