title: HF_variant_offtarget_WTCas9_A375_Dropout_RepA

first: John

description:
A375 cells were transduced with the HF-variant off-target library cloned into a vector containing WTCas9 and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data2_v2.xlsx

value: Skin

value: Dropout screen with HF variant off-target library using WTCas9 in A375 cells, replicate A


title: Kidney leukocytes D7

status: Public on Jul 21 2021

type: SRA

city: Hangzhou

first: QIXIA

last: SHEN

state: Zhejiang

address: Qinchun Rd.79, Hangzhou

country: China

institute: The first affiliated hospital, Hangzhou, China

library_source: transcriptomic

data_processing:
The analysis was done by Cell Ranger v3.0.2 at default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: For Kidney leukocytes D7 - barcodes.tsv, features.tsv, matrix.mtx.
Supplementary_files_format_and_content: For GSM4761000 and GSM4761003 - Kid_leukocytes_D15.txt (matrix table with raw gene counts for every gene and every cell; barcode-1 corresponds to GSM4761000,  barcode-2 corresponds to GSM4761003)

molecule: polyA RNA

organism: Mus musculus

source_name: a pooled sample from two kidney allografts

extract_protocol:
single cell were suspended in calcium-  and magnesium-free PBS containing 0.04% BSA after fluorescence-activated cell sorting. Then, single cell suspension went through cell counting and viability assessment using Countess II FL Automated Cell Counter.
Single cell encapsulation and cDNA libraries were prepared by Chromium™ Single Cell 5’ Reagent Kits and Chromium™ Single Cell A Chip Kit per manufacturer’s protocol.

tag: donor strain

value: BALB/c

tag: recipient strain

tag: age

value: 8 weeks old

tag: tissue

value: allografted kidneys

tag: cell type

value: allografted kidneys infiltrated leukocytes

tag: time

value: allografted kidneys were harvested on day 7 (D7)


title: TP309_seedling_R2_sRNA

city: Nanjing

first: Lili

last: Wang

address: Weigang No.1

institute: Nanjing Agricultural University

description: TP309_seedling_R2 sRNA-seq

data_processing:
Adapter sequences were trimed and clean reads with sizes ranging from 18 to 45 were mapped to MSU7.0 using Bowtie with parameter -v 0.
Annotated structure RNAs were excluded.
Read counts were normalized to RPTM.
Genome_build: MSU7.0

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: small RNA

growth_protocol: Rice plants grown in soil in jiangsu province

extract_protocol:
RNA was extrated using TRIzol method.
18-30nt small RNA was cut from PAGE gel.

value: seedling

tag: cultivar

tag: genotype

value: wildtype


title: 1 IRlox [TRA00038413]

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

country: USA

institute: Joslin Diabetes Center

data_processing:
Reads were aligned to the mouse genome using STAR.
Reads were counted with featureCounts.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: CSV file contains read counts.

extract_protocol:
RNA was extracted from a mixture of powdered Quad and gastrocnemius muscles using Trizol reagent (Invitrogen).
Stranded cDNA libraries with unique index tags for each sample (48 multiplexed) were made using a directional RNA-seq kit (Wafergen).

tag: strain background

value: mixed

value: Lox

value: IRlox

value: Muscle


title: Cas9NG_ABE8e_BRCA1_tiling_HAP1_Dropout_RepA

city: Cambridge

middle: G

last: Doench

state: MA

address: 75 Ames St.

department: Genetic Perturbation Platform

institute: Broad Institute

description:
HAP1 cells were transduced with the BRCA1 tiling library cloned into a vector containing NG-ABE8e and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data6_v2.xlsx

library_source: genomic

data_processing:
Library strategy: DNA-seq
Raw read counts were retrieved from sequencing data using PoolQ Version 3
Genome_build: GRCh38 primary assembly
Supplementary_files_format_and_content: Excel spreadsheets with guide-level read counts and library annotations

molecule: genomic DNA

organism: Homo sapiens

source_name: CML cell line

growth_protocol: Cells were cultured for 21 days. Every 2-3 cells were passaged and library representation was maintained >1000x.

extract_protocol:
Cells were lysed and genomic DNA was extracted using? Genomic DNA was PCR amplified using barcoded primers, then pooled and SPRI purified before submission for sequencing.
Oligonucleotide pools were synthesized by CustomArray. BsmBI recognition sites were appended to each sgRNA sequence  for cloning into the sgRNA expression plasmids, as well as primer sites to allow differential amplification of subsets from the same synthesis pool. The resulting amplicons were PCR-purified (Qiagen) and cloned into the library vector via Golden Gate cloning with Esp3I (Fisher Scientific) and T7 ligase (Epizyme)

treatment_protocol: If cells received drug treatment, drug was added to the cell culture media at each passage from D7 until D21.

value: Blood

tag: cell line

tag: treatment

value: untreated

tag: description

value: Dropout screen with ABE8e BRCA1 tiling library using Cas9-NG in HAP1 cells, replicate A


title: HF_variant_offtarget_HiFiCas9_A375_Dropout_RepB

description:
A375 cells were transduced with the HF-variant off-target library cloned into a vector containing HiFiCas9 and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data2_v2.xlsx

source_name: melanoma cell line

value: Dropout screen with HF variant off-target library using HiFiCas9 in A375 cells, replicate B


title: HF_variant_offtarget_WTCas9_A375_Dropout_RepB

value: Skin

value: Dropout screen with HF variant off-target library using WTCas9 in A375 cells, replicate B


title: Cas9NG_ABE8e_BRCA1_tiling_HAP1_Dropout_RepB


title: HF_variant_offtarget_HiFiCas9_A375_Dropout_RepA

value: Dropout screen with HF variant off-target library using HiFiCas9 in A375 cells, replicate A


title: AICAR d16+10p (129/MSM)

city: KYOTO

first: YAJING

last: LIU

address: KAWARAMATI53, SHIOGOIN,SAKYOUKU

country: Japan

institute: Center for iPS Cell Research and Application (CiRA), Kyoto University

description:
Bulk RNA-Seq data
MSM AICAR-2iL p10

data_processing:
The sequencing libraries were constructed using TruSeq Stranded mRNA Library Prep (Illumina, Inc.) 500 ng of total RNA and were sequenced in 79 cycle single read mode of HiSeq2500.
All sequenced reads passed quality filters were extracted to FASTQ format and demultiplexed to individual cells by barcodes using BCL2FASTQ Conversion Software v2.20.0.422.
FASTQ converted reads were then mapped to Ensembl GRCm38 release 100 reference cDNA and ncRNA sequences using Bowtie2 v2.2.5 with very-sensitive-local option. Among total of 68,196,501 reads 62,621,611 (91.8%) are successfully mapped and quantified as genes with threshold of MAPQ score ≥ 1.
Total of 34,489 genes (21,500 on average) are detected for 22 samples. Following analyses were performed by R ver. 3.6.3 after non-categorized limma voom normalization (Law et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: A matrix table of calculation of gene expression value and normalization were performed by RPKM for every sample and every gene

source_name: epiblast

growth_protocol: Primed mEpiSCs are culutred on MEF in FGF2 and Actinvin A before one day of reversion. We treated cells with Basal, 2iL, AICAR and AICAR+LIF four conditions. After 16 days, bulk cells were reculutred in 2iL condition. We collected d8 and d16 cells and reverted cells cultured in 2iL after several pasaages.

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (QIAGEN) and performed On-coloum DNase digestion (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: epiblast


title: MyLa Control

type: RNA

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

hyb_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).

scan_protocol: Agilent G2600A SureScan Microarray Scanner System.

data_processing: GeneSpring (Agilent), computed normalized signal intencity with 75%tile normalization.

source_name: MyLa Control

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol: Artemis1 medium plus 2% human serum.

value: MyLa

tag: mir

value: Empty


title: 7901_NC_transfected GC SGC7901 cells with lnc-LEMGC-overexpressed vector_48hr

city: Jinan

first: Peng

last: Gao

address: Wen Hua Xi Road 44

institute: Shandong University

description:
Gene expression after 48hr transfection with lnc-LEMGC-overexpressed vector in SGC7901 cells.
7901_P7

hyb_protocol: Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).  Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing:
Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. The 2 gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.
Genes that have values greater than or equal to lower cut-off: 100.0 in at least 1 out of 2 samples (“All Targets Value”) were chosen for data analysis.

source_name: Homo sapiens

label_protocol: Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit;Ds-cDNA labeling with NimbleGen one-color DNA labeling kit

growth_protocol: The cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (Gibco BRL, Grand Island, NY, USA). All cells were maintained in a humidified incubator at 37°C with 5% CO2 and confirmed to be Mycoplasma-negative.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: GC SGC7901 cells was transfected with lnc-LEMGC-overexpressed vector or NC for 48h.

tag: disease state

value: gastric cancer

value: lnc-LEMGC-overexpressed vector


title: 5 MIGIRKO [TRA00038417]

value: KO

value: MIGIRKO


title: 2 IGFRlox [TRA00038414]

value: mixed

value: Lox

value: IGFRlox


title: 4 IRIGFRlox [TRA00038416]

value: IRIGFRlox

value: Muscle


title: 7 days after IRI

city: Durham

first: Yoshihiko

last: Kobayashi

state: NC

address: 307 Research Dr

department: Cell Biology

institute: Duke University

data_processing:
FASTQ files were processed using dropSeqPipe v0.3 (https://hoohm.github.io/dropSeqPipe) and mapped on the GRCm38 genome reference with annotation version 91 to get UMI expression matrix files.
Genome_build: GRCm38.91

source_name: dissociated total kidney cells

extract_protocol:
Kidneys were dissociated with liberase TM, hyaluronidase, DNaseI at 37oC for 40 min, followed by incubation with 0.25% trypsin EDTA at 37oC for 30 min. Trypsin was inactivated using 10% fetal bovine serum in PBS. Cells were then resuspended in PBS supplemented with 0.01% bovine serum albumin then filtered through 40 µm strainer and utelized for Drop-seq
DNA polymerase for pre-amplification step (1 cycle of 95°C for 3 min, 15-17 cycles of 98°C for 15 sec, 65°C for 30 sec, 68°C for 4 min and 1 cycle of 72°C for 10 min) was replaced by Terra PCR Direct Polymerase (#639271, Takara). The other processes were performed as described in the original Drop-seq protocol. Sequencing was performed using Hiseq X ten.
single-cell RNA-seq (Drop-seq)

treatment_protocol: Ischemia-reperfusion injury was induced by the retroperitoneal approach on the left kidney for 30 min by an atraumatic vascular clip (Roboz, RS-5435). Kidneys were harvested at 6 hours and 1, 7, and 21 days after the surgery.

value: dissociated total kidney cells

value: 9 weeks


title: 21 days after IRI

value: 13 weeks


title: 7901_NC_transfected GC SGC7901 cells with NC_48hr

description:
Gene expression after 48hr transfection with NC in SGC7901 cells.
7901_C1

value: control


title: HF_variant_offtarget_eCas9_A375_Dropout_RepA

description:
A375 cells were transduced with the HF-variant off-target library cloned into a vector containing eCas9 and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data2_v2.xlsx

value: Skin

value: untreated

value: Dropout screen with HF variant off-target library using eCas9 in A375 cells, replicate A


title: Primed mEpiSCs (129/MSM)

description:
Bulk RNA-Seq data
129/MSM primed

value: epiblast


title: 1 day after IRI


title: AICAR d16

description:
Bulk RNA-Seq data
Oct4 AICAR d16


title: TP309_seedling_R1_sRNA

description: TP309_seedling_R1 sRNA-seq

value: seedling

value: wildtype


title: 2iL d16

description:
Bulk RNA-Seq data
Oct4 2iL d16


title: Cas9NG_CBE_BRCA1_tiling_MELJUSO_RepC_Cisplatin

description:
Meljuso cells were transduced with the BRCA1 tiling library cloned into a vector containing NG-CBE and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the presence of Cisplatin for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data5_v2.xlsx

value: MELJUSO

value: 1uM Cisplatin

value: Cisplatin screen with CBE BRCA1 tiling library using Cas9-NG in Meljuso cells, replicate C


title: AICAR+LIF d16

description:
Bulk RNA-Seq data
Oct4 A+L d16


title: Homeostasis


title: MyLa miR-26a

source_name: MyLa miR-26a

label_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).

value: MyLa


title: basal d16

description:
Bulk RNA-Seq data
Oct4 basal d16


city: Clayton

first: Seungmin

last: Ham

state: Victoria

address: 27-31, Wright Street

department: Obstetrics and Gynaecology

country: Australia

institute: Monash University

description: Keloid fibroblasts FST at day 5 16-13595 16-13595

data_processing:
Data was processed with RNAsik pipeline (https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe - unknown version).
Each fastq file was mapped to reference genome using STAR
Aligned BAM files were then counted against GTF using featureCounts
The raw counts file was loaded into Degust (http://degust.erc.monash.edu/) for differential gene expression analysis
Genome_build: Ensembl reference genome is Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa, GTF file was Homo_sapiens.GRCh38.85.gtf.gz
Supplementary_files_format_and_content: tab seperated file containing the raw counts for each sample

source_name: Dermal fibroblasts

growth_protocol:
Biopsy samples were finely minced and plated out for culture in T25 or T75 flasks. Primary human dermal fibroblasts were grown in DMEM/F12 (Gibco, Cat# 11039021, Scoresby, Australia) containing 10% Fetal Bovine Serum (Gibco, Cat# 10437028, Scoresby, Australia) and 1% Penicillin-Streptomycin (5,000 U/mL) (Gibco, Cat# 15070063, Scoresby, Australia). All fibroblasts were cultured at 37°C in 5% CO2 and media were changed twice a week.
When cultures reached between 80 and 90% confluency, fibroblasts were plated in 10 cm dishes (Corning, Melbourne, Australia) at a concentration of 3 x 10^5 cells / 10 ml per dish and starved for 24 hours prior to treatment.

extract_protocol:
Total RNA were extracted using  RNeasy Mini Kit according to manufacturer's instructions.
Libraries were prepared according to Illumina's instructions at MHTP Medical Genomics Facility.
RNA-seq at MHTP Medical Genomics Facility

treatment_protocol: After serum starving, normal and keloid fibroblasts were cultured for 1 or 5 days with/without follistatin treatment.

value: primary keloid dermal fibroblasts

tag: passages

value: follistatin (FST)

value: Day 5 after treatment

value: Human skin


title: Cas9NG_CBE_BRCA1_tiling_MELJUSO_RepB_Cisplatin

value: Cisplatin screen with CBE BRCA1 tiling library using Cas9-NG in Meljuso cells, replicate B


title: Cas9NG_CBE_BRCA1_tilingMELJUSO_RepA_Cisplatin

value: Cisplatin screen with CBE BRCA1 tiling library using Cas9-NG in Meljuso cells, replicate A


title: AICAR+LIF d16+10p (129/MSM )

description:
Bulk RNA-Seq data
MSM A+L-2iL p10


title: AICAR+LIF d8

description:
Bulk RNA-Seq data
Oct4 A+L d8


description: Keloid fibroblasts FST at day 5 16-13594 16-13594


title: Cas9NG_CBE_BRCA1_tiling_MELJUSO_RepC_Dropout

description:
Meljuso cells were transduced with the BRCA1 tiling library cloned into a vector containing NG-CBE and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data5_v2.xlsx

value: Dropout screen with CBE BRCA1 tiling library using Cas9-NG in Meljuso cells, replicate C


title: HF_variant_offtarget_eCas9_A375_Dropout_RepB

value: Skin

value: Dropout screen with HF variant off-target library using eCas9 in A375 cells, replicate B


title: AICAR d8

description:
Bulk RNA-Seq data
Oct4 AICAR d8


title: 6 hrs after IRI

value: dissociated total kidney cells

value: 8 weeks


description: Normal fibroblasts FST at day 5 16-13592 16-13592

value: primary normal dermal fibroblasts


title: Cas9NG_CBE_BRCA1_tiling_HAP1_Dropout_RepC

description:
HAP1 cells were transduced with the BRCA1 tiling library cloned into a vector containing NG-CBE and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data5_v2.xlsx

value: Blood

value: untreated

value: Dropout screen with CBE BRCA1 tiling library using Cas9-NG in HAP1 cells, replicate C


title: 2iL d8

description:
Bulk RNA-Seq data
Oct4 2iL d8

value: epiblast


title: Cas9NG_CBE_BRCA1_tiling_MELJUSO_RepA_Dropout

value: MELJUSO

value: Dropout screen with CBE BRCA1 tiling library using Cas9-NG in Meljuso cells, replicate A


title: basal d8

description:
Bulk RNA-Seq data
Oct4 basal d8


description: Normal fibroblasts FST at day 5 16-13590 16-13590

value: follistatin (FST)


title: Cas9NG_CBE_BRCA1_tiling_HAP1_Dropout_RepB

value: Dropout screen with CBE BRCA1 tiling library using Cas9-NG in HAP1 cells, replicate B


description: Normal fibroblasts FST at day 5 16-13591 16-13591

value: Day 5 after treatment

value: Human skin


title: Keloid fibroblasts vc at day 5 16-13589

description: Keloid fibroblasts vc at day 5 16-13589 16-13589

value: primary keloid dermal fibroblasts

value: vehicle control (vc)


title: A769662+LIF d16+10p

description:
Bulk RNA-Seq data
Oct4 A769662+lif-2iL p10


title: metformin+LIF d16+10p

description:
Bulk RNA-Seq data
Oct4 met+lif-2iL p10


title: Cas9NG_CBE_BCL2_tiling_MOLM13_Venetoclax_RepC

description:
MOLM-13 cells were transduced with the BCL2 tiling library cloned into a vector containing NG-CBE and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the presence of Venetoclax for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data7_v2.xlsx

source_name: AML cell line

value: 62.5 nM Venetoclax

value: Venetoclax screen with CBE BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate C


title: Keloid fibroblasts vc at day 5 16-13588

description: Keloid fibroblasts vc at day 5 16-13588 16-13588


title: Normal fibroblasts vc at day 5 16-13586

description: Normal fibroblasts vc at day 5 16-13586 16-13586


title: Cas9NG_CBE_BCL2_tiling_MOLM13_Venetoclax_RepB

value: Venetoclax screen with CBE BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate B


title: Normal fibroblasts vc at day 5 16-13585

description: Normal fibroblasts vc at day 5 16-13585 16-13585


title: AICAR d16+10p

description:
Bulk RNA-Seq data
Oct4 AICAR-2iL p10


title: A769662 d16+10p

description:
Bulk RNA-Seq data
Oct4 A769662-2iL p10


title: AICAR+LIF d16+10p

description:
Bulk RNA-Seq data
Oct4 A+L-2iL p10


title: Cas9NG_CBE_BCL2_tiling_MOLM13_Venetoclax_RepA

value: Venetoclax screen with CBE BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate A


title: Cas9NG_CBE_BCL2_tiling_MOLM13_Dropout_RepC

description:
MOLM-13 cells were transduced with the BCL2 tiling library cloned into a vector containing NG-CBE and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data7_v2.xlsx

value: Dropout screen with CBE BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate C


title: AICAR+LIF d16+3p

description:
Bulk RNA-Seq data
Oct4 A+L-2iL p3


description: Keloid fibroblasts FST at day 5 16-13593 16-13593


title: Cas9NG_CBE_BRCA1_tiling_MELJUSO_RepB_Dropout

value: Skin

value: Dropout screen with CBE BRCA1 tiling library using Cas9-NG in Meljuso cells, replicate B


title: Normal fibroblasts vc at day 5 16-13584

description: Normal fibroblasts vc at day 5 16-13584 16-13584

value: primary normal dermal fibroblasts


title: AICAR d16+3p

description:
Bulk RNA-Seq data
Oct4 AICAR-2iL p3

value: epiblast


description: Keloid fibroblasts FST at day 1 KeloidFST3 KeloidFST3

value: Day 1 after treatment


title: Cas9NG_CBE_BCL2_tiling_MOLM13_Dropout_RepA

value: Blood

value: untreated

value: Dropout screen with CBE BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate A


title: Cas9NG_CBE_BCL2_tiling_MOLM13_Dropout_RepB

value: Dropout screen with CBE BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate B


title: AICAR+LIF d16+2p

description:
Bulk RNA-Seq data
Oct4 A+L-2iL p2


title: Cas9NG_ABE8e_BCL2_tiling_MOLM13_Venetoclax_RepB

description:
MOLM-13 cells were transduced with the BCL2 tiling library cloned into a vector containing NG-ABE8e and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the presence of Venetoclax for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data7_v2.xlsx

value: Venetoclax screen with ABE8e BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate B


title: Cas9NG_ABE8e_BCL2_tiling_MOLM13_Venetoclax_RepC

value: Venetoclax screen with ABE8e BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate C


title: AICAR d16+2p

description:
Bulk RNA-Seq data
Oct4 AICAR-2iL p2


title: Keloid fibroblasts vc at day 5 16-13587

description: Keloid fibroblasts vc at day 5 16-13587 16-13587

value: primary keloid dermal fibroblasts

value: vehicle control (vc)

value: Day 5 after treatment

value: Human skin


title: Primed mEpiSCs (Oct4GIP)

description:
Bulk RNA-Seq data
Oct4 primed


description: Normal fibroblasts FST at day 1 NormalFST3 NormalFST3

value: follistatin (FST)


title: Cas9NG_ABE8e_BCL2_tiling_MOLM13_Venetoclax_RepA

value: 62.5 nM Venetoclax

value: Venetoclax screen with ABE8e BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate A


title: Cas9NG_CBE_BRCA1_tiling_HAP1_Dropout_RepA

value: Dropout screen with CBE BRCA1 tiling library using Cas9-NG in HAP1 cells, replicate A


title: Naïve mESCs (Rex1-GFP)

description:
Bulk RNA-Seq data
Rex1 naïve


description: Keloid fibroblasts FST at day 1 KeloidFST2 KeloidFST2


description: Normal fibroblasts FST at day 1 NormalFST1 NormalFST1

value: primary normal dermal fibroblasts


title: CAR-T+E-3

city: Beijing

first: Ligong

last: Chen

state: China

address: No.1, Qinghuayuan, Haidian District

department: School of Pharmaceutical Sciences

institute: Tsinghua University

description: Tumor samples from cancer xenograft mice injected with the combination of CAR-T cells and PSC-derived eosinophils (E)

data_processing:
Fastq reads were trimmed for adaptor sequence  and aligned to mouse reference genome (mm10) using TopHat with default parameters
Counting and FPKM values were calculated with cuffquant and cuffnorm respectively with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files include FPKM values for mouse genes in each Sample. Human gene expression was not evaluated.

organism:
Homo sapiens
Mus musculus

source_name: mouse blood cell

extract_protocol:
total RNA
NEB England BioLabs, E7530L

treatment_protocol: tumors with immune cell infusion were digested into single cell suspensions by Collagenase, Type IV (Gibco, Cat:17104-019).These tumor cells were collected for RNA-seq assay.

value: tumor from cancer xenograft mice

tag: cell line used for xenograft

value: Human HepG2

tag: condition

value: CAR-T+E


title: Cas9NG_ABE8e_BCL2_tiling_MOLM13_Dropout_RepA

description:
MOLM-13 cells were transduced with the BCL2 tiling library cloned into a vector containing NG-ABE8e and a puromycin resistance cassette. Cells were selected with puromycin from day 2 post-transduction to day 7 post-transduction, then passaged in the absence of drug for the remainder of the screen. At 21 days post-transduction, cells were collected; genomic DNA from these cells was isolated, and the guides were PCR-amplified and sequenced.
processed data in: Supplementary_Data7_v2.xlsx

value: Blood

value: untreated

value: Dropout screen with ABE8e BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate A


title: CAR-T+E-2


title: Cas9NG_ABE8e_BCL2_tiling_MOLM13_Dropout_RepB

value: Dropout screen with ABE8e BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate B


description: Keloid fibroblasts vc at day 1 KeloidVC3 KeloidVC3

value: Day 1 after treatment


description: Normal fibroblasts FST at day 1 NormalFST2 NormalFST2


title: Cas9NG_ABE8e_BCL2_tiling_MOLM13_Dropout_RepC

value: Dropout screen with ABE8e BCL2 tiling library using Cas9-NG in MOLM13 cells, replicate C


description: Keloid fibroblasts vc at day 1 KeloidVC2 KeloidVC2

value: primary keloid dermal fibroblasts

value: vehicle control (vc)


description: Keloid fibroblasts vc at day 1 KeloidVC1 KeloidVC1

value: Human skin


title: CAR-T-2

description: Tumor samples from cancer xenograft mice injected with CAR-T cells

value: CAR-T


description: Normal fibroblasts vc at day 1 NormalVC3 NormalVC3


title: CAR-T-3


description: Normal fibroblasts vc at day 1 NormalVC2 NormalVC2


description: Keloid fibroblasts FST at day 1 KeloidFST1 KeloidFST1

value: follistatin (FST)


description: Normal fibroblasts vc at day 1 NormalVC1 NormalVC1


title: U3-3days_3

city: Edinburgh

first: Hywel

last: Dunn-Davies

address: Max Born Crescent

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Raw reads were reverse complemented using FASTX-Toolkit,  and trimmed using Trimmomatic
Reads were aligned to the human genome using STAR, and rRNA and tRNA overlaps were filtered out using bedtools (using the ensembl release 77 reference annotation for rRNAs and GtRNAdb for tRNAs)
Gene level quantification was performed using htseq-count (with options -f bam -r pos -s yes -t exon -i gene_name -m union)
Differential expression analysis was carried out using DESeq2
Genome_build: Ensembl human GRCh38 assembly, release 77
Supplementary_files_format_and_content: Results of differential expression analysis and htseq-count files  are provided as tab separated text files

growth_protocol: HEK cells were grown in DMEM media with 10% FBS.

extract_protocol:
Cells were collected 2 and 3 days after transfection and total RNA was extracted
cDNA library was prepared from PolyA selected RNA using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina following the manufacturer's instructions
strand-specific library preparation for Illumina RNA-Seq

treatment_protocol: A morpholino oligo was used to deplete the cells of U3 snoRNA, mock treated cells were used as the control

value: HEK

tag: mutation

value: U3 depletion using a morpholino oligo over 3 days


title: FigS3DE_23997_105WCE

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

institute: University of Oxford

description: Arrested in G2 (Nocodazole) at 37˚C

data_processing:
Library sequencing was carried out on the Ion Torrent Proton
The quality of the raw sequence data was examined using FastQC and trimming of reads was carried out using fastx_trimmer
Any reads smaller than 50bp were removed using ‘Filter FASTQ’
The final reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, SGD) or Candida glabrata genome (CBS138, genolevures) using Bowtie2 with the default (--sensitive) parameters
To generate an alignment in which all the sequences exclusively align to the Saccharomyces cerevisiae genome, the whole reads were first aligned to Candida glabrata genome and the unaligned reads were retrieved as a separate Fastq file. Subsequently, these unaligned reads were re-aligned to Saccharomyces cerevisiae genome and the resulting aligned BAM file therefore contained reads that were unique to Saccharomyces cerevisiae. A same strategy was used to generate alignments unique to Candida glabrata.
Genome_build: SacCer3 or Candida glabrata (ASM254v2)
Supplementary_files_format_and_content: bigwig files

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells

growth_protocol: Yeast cells were grown in YPD to reach a density of 0.3-0.6 OD600.

extract_protocol:
To crosslink cells, 45ml of yeast culture was mixed with 4.2ml of fixation solution (50mM Tris-HCl pH 8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 30% Formaldehyde) and incubated at 18°C for 30 minutes. The crosslinking reaction was quenched by incubating with 2ml of 2.5M Glycine for 5 min. Fixed cells were harvested, washed with ice-cold PBS and re-suspended in 1ml of ChIP lysis buffer (50mM Hepes-KOH pH 8.0, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF, Roche protease inhibitor). For each ChIP, 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells were pelleted and re-suspended in 0.3ml of ChIP lysis buffer. Cells were mixed with glass beads and disrupted by FastPrep®-24 (MP Biomedicals, USA). The entire lysis was collected and sonicated at 4°C for 40 minutes using a Bioruptor (Diagenode, Belgium). The cell debris were removed by centrifugation and supernatants containing sheared chromatin with a size range from 100-800bp were adjusted to a final volume of 1ml with ChIP lysis buffer. Extracts were pre-cleared for 1 hour at 4°C with 30µl of Protein G Dynabeads (Invitrogen). 80µl of supernatant was taken as whole cell extract (W) and stored at -80°C. Five µg of anti-PK antibody (Bio-Rad) and 50 µl of Protein G Dynal beads (Invitrogen) was used for immunoprecipitation (6 hours-overnight, rotation at 4°C). The beads were subsequently washed for 5 minutes with the following buffers: 2Ã—ChIP lysis buffer; 3x ChIP high-salt lysis buffer (50mM Hepes-KOH pH 8.0, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF); 2Ã—ChIP wash buffer (10mM Tris-HCl pH 8.0, 0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA, 1mM PMSF) and 1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl). The immunoprecipitated chromatin was eluted by incubation of beads with 120µl of TES buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 1% SDS) at 65°C for 15 minutes. The supernatants were collected and termed the IP sample. The whole cell extract sample (W) was mixed with 40µl of TES3 buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 3% SDS). Both samples were de-crosslinked at 65°C overnight. RNA was degraded by incubating with 2-µl of RNAse A (10mg/ml, Roche) at 37°C for 1 hour and protein was subsequently removed by incubation with 10µl of Proteinase K (18mg/ml, Roche) at 65°C for 2 hours. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
NEBNext Fast DNA Library Prep set for Ion Torrent, E6270

tag: sac_cer strain

value: sac_cer strain:K23997

tag: can_gla strain

value: can_gla strain:K23308

tag: antibody

value: none (input)


title: U3-3days_2


title: U3-3days_1


title: U3-2days_3

value: U3 depletion using a morpholino oligo over 2 days


title: FigS3DE_23997_75WCE

description: Arrested in G2 (Nocodazole) at 37˚C


title: ON LPS cKO Input rep3 m6A-seq

city: Rehovot

first: Ziv

last: Shulman

address: Herzl St 234

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Mars-seq: Reads were trimmed using Cutadapt
Mars-seq and m6A-IP: Reads were aligned to the genome using STAR
Mars-seq: Quantification was done using htseq-count as previously described in R. Kohen, BMC Bioinformatics, 2019.
m6A-IP: Normalization of paired libraries insert size was performed using in-house python scripts, between pairs of INPUT-IP samples. Alignment sorting and indexing were performed separately with samtools (V. 1.3.1) (Li et al. Bioinformatics, 2009).
m6A-IP: Identification of putative m6A sites was performed by assigning peak over input (POI) and peak over median (POM) scores to each site, as previously published (Schwartz et al, Cell 2014)
Genome_build: Mars-seq: mm10, m6A-IP: mm9
Supplementary_files_format_and_content: Excel file with Deseq2 output
Supplementary_files_format_and_content: Text file with filtered m6A-peaks 1
Supplementary_files_format_and_content: Text file with filtered m6A-peaks 2

source_name: B cells

extract_protocol:
Total RNA was harvested from activated cells using Trizol. Enrichment for PolyA RNA was done twice using mRNA mRNA direct kit and checked using TapeStation (Agilent). PolyA-selected RNA was barcoded and immunoprecipitated in two rounds using anti-m6A polyclonal antibody bound to magnetic protein-G beads and protein-A beads
Libraries were prepared as previously described (Garcia-Campos et al. Cell, 2019). Briefly, eluted RNA was reverse transcribed and an adapter was added using Superscript III reverse transcriptase (Thermo Fisher, 18080093). A second adaptor was added to the cDNA by ligation with T4 RNA Ligase 1 (NEB, M0437M). Following clean-up with MyOne Silane beads, the cDNA library was amplified in a PCR using KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2601).Libraries were sequenced on an Illumina NextSeq 500 machine.

tag: cell type

value: Overnight LPS activated B cells

tag: mouse strain

value: AIDcre Mettl3-flox/flox


title: ON LPS cKO Input rep2 m6A-seq

tag: genotype


title: ON LPS Ctrl IP rep3 m6A-seq

value: AIDcre Mettl3-flox/+


title: ON LPS cKO Input rep1 m6A-seq


title: FigS3DE_23997_105IP

description: Arrested in G2 (Nocodazole) at 37˚C

value: anti-PK antibody (Bio-Rad)


title: ON LPS Ctrl Input rep3 m6A-seq


title: Mock_3

value: Mock control


title: CAR-T+E-1

value: tumor from cancer xenograft mice

value: Human HepG2

value: CAR-T+E


title: FigS3DE_23997_75IP

description: Arrested in G2 (Nocodazole) at 37˚C


title: U3-2days_1


title: ON LPS Ctrl IP rep1 m6A-seq


title: FigS4BC_25387IP

description: Cycling cells

value: sac_cer strain:K25387


title: FigS4BC_22009WCE

description: Cycling cells

value: sac_cer strain:K22009


title: ON LPS Ctrl Input rep2 m6A-seq


title: Mock_2


title: FigS4BC_25387WCE

description: Cycling cells


title: ON LPS Ctrl IP rep2 m6A-seq


title: FigS4BC_22009IP

description: Cycling cells


title: U3-2days_2


title: CAR-T-1

value: CAR-T


title: FigS4BC_22005WCE

description: Cycling cells

value: sac_cer strain:K22005


title: Mock_1

value: HEK


title: ON LPS cKO IP rep3 m6A-seq


title: F5

city: Stockholm

first: Szabolcs

last: Éliás

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institute

data_processing:
Base-calling was performed using Illumina HiSeq Control/Real Time Analysis software.
Base-call files were demultiplexed and converted to fastq files using bcl2fastq version 2.17.1.14.
Sequence reads were aligned to the human genome version hg38 using STAR version 2.5.2b with the GENCODE version 25 annotation file and with the settings ‘--clip3pAdapterSeq <adapters>’ for adapter trimming and ‘--quantMode  TranscriptomeSAM GeneCounts’ for counting read pairs on the gene level.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file containing counts of read pairs for GENCODE version 25 genes

source_name: Peripheral Blood

growth_protocol: Primary cells from human peripheral blood.

extract_protocol:
Cells were washed with PBS and lysed in QIAzol Lysis Reagent (Qiagen) by vortexing and incubating for 5 min at 20°C. Lysates were stored at -80°C until RNA extraction. RNA was extracted with the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration was determined on a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific) and RNA quality was controlled on a 2100 Bioanalyzer instrument (Agilent Technologies) using an Agilent RNA 6000 Pico Kit. RNA integrity numbers (RIN) were 8.5±0.3 (mean±SD).
Libraries were prepared in one batch with the TruSeq Stranded mRNA HT kit (Illumina) with Dual Indexing adapters and Ambion ERCC Spike-In Control (Thermo Fisher Scientific). Samples were allocated to sequencing indexes and -lanes in a balanced fashion to control for potential batch effects (7-8 samples/lane). Library concentration was determined on a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Library size and quality were measured on a 2100 Bioanalyzer instrument (Agilent Technologies) using an Agilent High Sensitivity DNA Kit. Libraries were quantified with the KAPA Library Quantification Kit (KAPA Biosystems). Sequencing was performed on a HiSeq 2500 Sequencing Platform (Illumina; High Output Run) with 76 nt paired-end reads.

treatment_protocol: Peripheral blood mononuclear cell (PBMC) isolation by Ficoll gradient, followed by magnetic activated cell sorting (MACS) of given CD4 T cell sub-populations as follows. Naive, total (bulk) and memory CD4 T cells were isolated in parallel by negative magnetic isolation according to the manufacturer's protocol (Miltenyi Biotec). From an aliquot of total CD4 T cells, GM-CSF producing and GM-CSF negative cells were subsequently isolated without restimulation using the GM-CSF Secretion Assay - Cell Enrichment and Detection Kit (PE), human (Miltenyi Biotec), according to the manufacturer’s instructions

tag: tissue

value: Peripheral Blood

value: Memory CD4 T cells

tag: donor

value: F

tag: gender

value: male


title: ON LPS cKO IP rep2 m6A-seq

value: Overnight LPS activated B cells


title: FigS4BC_22005IP

description: Cycling cells

value: can_gla strain:K23308


title: ON LPS cKO IP rep1 m6A-seq

value: AIDcre Mettl3-flox/flox


title: FigS4BC_19012WCE

description: Cycling cells

value: sac_cer strain:K19012

value: none (input)


title: F4

value: Bulk CD4 T cells


title: F3

value: GM-CSF negative CD4 T cells


title: Igf2bp3 2w_WT DZ rep3 MARS-seq

extract_protocol:
mRNA was extracted from sorted cells using mRNA direct kit (Invitrogen) and mRNA from each sample was barcoded during reverse transcription and pooled.
Libraries were prepared using a bulk adaptation of the previously described protocol (Keren-Shaul et al. Nat. Protoc, 2019 and Jaitin et al. Science, 2014).Following Agencourt Ampure XP bead cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR for the ACTB gene as previously described. Sequencing was done using a Nextseq 75 cycle high output kit (Illumina; paired end sequencing).

value: Germinal center dark zone B cells

value: Wild type


title: F2

value: GM-CSF positive CD4 T cells


title: FigS4A_27751WCE

description: Arrested in G2 (Nocodazole) at 37˚C in the presence of auxin

value: sac_cer strain:K27751


title: Igf2bp3 2w_WT DZ rep2 MARS-seq


title: FigS4BC_19012IP

description: Cycling cells

value: anti-PK antibody (Bio-Rad)


title: Igf2bp3 2w_WT DZ rep1 MARS-seq


title: ON LPS Ctrl Input rep1 m6A-seq

value: AIDcre Mettl3-flox/+


title: Igf2bp3 2w_KO DZ rep4 MARS-seq


title: FigS4A_22001WCE

value: sac_cer strain:K22001


title: E5

value: Peripheral Blood

value: Memory CD4 T cells

value: E


title: Igf2bp3 2w_KO DZ rep3 MARS-seq


title: FigS4A_27751IP


title: E4

value: male


title: FigS4A_22001IP

value: can_gla strain:K23308


title: Igf2bp3 2w_KO DZ rep2 MARS-seq


title: Igf2bp3 2w_KO DZ rep1 MARS-seq


title: E3


title: E2


title: AIDcre Ythdf2flox 1w Ctrl DZ rep2 MARS-seq

value: AIDcre Ythdf2-flox/+


title: FigS3GBottom_699

description: Cycling cells shifted to 37˚C for 2 hours

value: sac_cer strain:K699


title: D5

value: D


title: E1

value: Naive CD4 T cells


title: F1

value: F


title: FigS3GTop_699

value: none (input)


title: D4

value: Bulk CD4 T cells


title: AIDcre Mettl3flox 2w Ctrl LZ rep3 MARS-seq

value: Germinal center light zone B cells


title: D3

value: GM-CSF negative CD4 T cells


title: FigS3F_24031_105WCE

description: Arrested in G2 (Nocodazole) at 37˚C

value: sac_cer strain:K24031


title: AIDcre Ythdf2flox 1w Ctrl DZ rep1 MARS-seq

value: Germinal center dark zone B cells


title: D2

value: GM-CSF positive CD4 T cells


title: FigS3F_24031_105IP

description: Arrested in G2 (Nocodazole) at 37˚C

value: anti-PK antibody (Bio-Rad)


title: D1

value: Peripheral Blood


title: C5

value: Memory CD4 T cells

value: C


title: AIDcre Ythdf2flox 1w cKO DZ rep1 MARS-seq

value: AIDcre Ythdf2-flox/flox


title: FigS3GBottom_8326

value: sac_cer strain:K8326


title: FigS3F_24031_75IP

description: Arrested in G2 (Nocodazole) at 37˚C

value: can_gla strain:K23308


title: FigS3F_24031_75WCE

description: Arrested in G2 (Nocodazole) at 37˚C


title: FigS3F_23997_105WCE

description: Arrested in G2 (Nocodazole) at 37˚C

value: sac_cer strain:K23997


title: C4

value: male


title: AIDcre Mettl3flox 2w Ctrl DZ rep2 MARS-seq

value: AIDcre Mettl3-flox/+


title: FigS3GTop_24032

value: sac_cer strain:K24032

value: none (input)


title: FigS3F_23997_105IP

description: Arrested in G2 (Nocodazole) at 37˚C


title: C3


title: FigS3F_23997_75WCE

description: Arrested in G2 (Nocodazole) at 37˚C


title: C2


title: C1

value: Naive CD4 T cells


title: AIDcre Mettl3flox 2w Ctrl LZ rep1 MARS-seq

value: Germinal center light zone B cells


title: FigS3F_23997_75IP

description: Arrested in G2 (Nocodazole) at 37˚C


title: AIDcre Ythdf2flox 1w cKO DZ rep2 MARS-seq


title: AIDcre Mettl3flox 2w cKO LZ rep3 MARS-seq

value: AIDcre Mettl3-flox/flox


title: AIDcre Mettl3flox 2w Ctrl DZ rep1 MARS-seq

value: Germinal center dark zone B cells


title: AIDcre Mettl3flox 2w Ctrl DZ rep3 MARS-seq


title: B5

value: B


title: AIDcre Mettl3flox 2w cKO DZ rep3 MARS-seq


title: AIDcre Mettl3flox 2w cKO LZ rep2 MARS-seq


title: B3

value: GM-CSF negative CD4 T cells


title: B2

value: Peripheral Blood

value: GM-CSF positive CD4 T cells


title: AIDcre Mettl3flox 2w cKO LZ rep1 MARS-seq


title: B1


title: FigS3F_22009_105WCE

description: Arrested in G2 (Nocodazole) at 37˚C

value: sac_cer strain:K22009


title: FigS3F_22005_105WCE

description: Arrested in G2 (Nocodazole) at 37˚C

value: sac_cer strain:K22005


title: FigS3F_22009_75IP

description: Arrested in G2 (Nocodazole) at 37˚C

value: anti-PK antibody (Bio-Rad)


title: A4

value: Bulk CD4 T cells

value: A


title: FigS3F_22009_105IP

description: Arrested in G2 (Nocodazole) at 37˚C

value: can_gla strain:K23308


title: A3

value: male


title: FigS3F_22005_105IP

description: Arrested in G2 (Nocodazole) at 37˚C


title: A2


title: AIDcre Mettl3flox 2w cKO DZ rep1 MARS-seq


title: AIDcre Mettl3flox 1w Ctrl LZ rep4 MARS-seq

value: AIDcre Mettl3-flox/+


title: FigS3F_22009_75WCE

description: Arrested in G2 (Nocodazole) at 37˚C

value: none (input)


title: AIDcre Mettl3flox 2w cKO DZ rep2 MARS-seq


title: AIDcre Mettl3flox 1w Ctrl DZ rep4 MARS-seq


title: AIDcre Mettl3flox 1w Ctrl LZ rep3 MARS-seq


title: FigS3DE_22005_105WCE

description: Arrested in G2 (Nocodazole) at 37˚C


title: FigS3F_22005_75IP

description: Arrested in G2 (Nocodazole) at 37˚C


title: A1

value: Naive CD4 T cells


title: B4


title: AIDcre Mettl3flox 1w Ctrl DZ rep3 MARS-seq


title: FigS3DE_22005_105IP

description: Arrested in G2 (Nocodazole) at 37˚C


title: AIDcre Mettl3flox 1w Ctrl LZ rep2 MARS-seq

value: Germinal center light zone B cells


title: F_5_r

data_processing:
Base-calling was performed using Illumina HiSeq Control/Real Time Analysis software.
Base-call files were demultiplexed and converted to fastq files using bcl2fastq version 2.17.1.14.
Fastq files were adapter-trimmed using scythe version 0.991 and quality-trimmed using sickle version 1.33.
Trimmed fastq files were aligned to the human genome version hg38 using bowtie version 2.3.0 with the ‘--very-sensitive’ setting.
Bam files were sorted, indexed and filtered using samtools version 0.1.19 to remove duplicates, alignments with a mapping score below 10, and alignments not mapped to chromosomes 1-22, X or Y.
Peak-calling was performed using the ‘findPeaks’ script from the Homer suite version 4.9.1 with the '-style factor' setting.
A consensus peak-set containing genomic regions with reproducible accessibility was generated as described in the accompanying publication.
Reads in the genomic regions defined by the consensus peak-set were counted for each sample using the featureCounts version 1.5.2 with the settings ‘-s 0 –minOverlap 1 --fracOverlap 0.5’.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file containing read counts at reproducibly accessible genomic regions (consensus peaks)

extract_protocol:
Nuclear isolation was carried out according to Buenrostro et al. 2013 (PMID: 24097267).
Library construction including tagmentation and PCR amplification was performed according to Buenrostro et al. 2013 (PMID: 24097267) followed by additional gel size selection of DNA in the size range of 150-230 base pairs.

treatment_protocol: Peripheral blood mononuclear cell (PBMC) isolation by Ficoll gradient, followed by magnetic activated cell sorting (MACS) of given CD4 T cell sub-populations as follows. Naive, total (bulk) and memory CD4 T cells were isolated in parallel by negative magnetic isolation according to the manufacturer's protocol (Miltenyi Biotec). From an aliquot of total CD4 T cells, GM-CSF producing and GM-CSF negative cells were subsequently isolated without restimulation using the GM-CSF Secretion Assay - Cell Enrichment and Detection Kit (PE), human (Miltenyi Biotec), according to the manufacturer’s instructions. For each isolated cell type and donor, three technical replicates (denoted “p”, “q”, “r”; except donor A, two technical replicates) with 50000 cells each were further processed.

value: Memory CD4 T cells

value: F


title: FigS3DE_22005_75WCE

description: Arrested in G2 (Nocodazole) at 37˚C


title: AIDcre Mettl3flox 1w Ctrl LZ rep1 MARS-seq


title: KHA082120_016

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

description: U2OS human osteosarcoma cells with doxycycline-inducible expression of EGFP-FOXM1 fusion protein, adherent epithelial cells, pre-treated with 1 ug/mL doxycycline for 16 hours, treated with 1 ug/mL doxycycline and 50 uM STL427944 for 24 hours, RNA purified immediately after treatment

data_processing:
Raw reads were aligned to the reference genome using STAR.
ENSEMBL gene expression was quantified using FeatureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text tables

source_name: C3Luc Doxy+STL

growth_protocol: Cells were grown in DMEM with 10% FBS, 4.5 g/L glucose, 4 mM L-glutamine, 1 mM sodium pyruvate, 100 U/mL penicillin, and 100 ug/mL streptomycin

extract_protocol:
Cell culture samples were collected immediately after treatment and lysed in TRIzol. Phase separation was performed with chloroform according to manufacturer's instructions. Aqueous phase was collected and used for RNA purification with Invitrogen PureLink RNA Mini Kit with on-column DNAse treatment according to manufacturer's protocol.
CORALL (Lexogen)

treatment_protocol: Growth medium was aspirated from cells and replaced with complete growth medium containing selected concentrations of treatment compounds. Cells were incubated in presence of treatment compounds in CO2 incubator at 37 degrees C for 24 hours

tag: cell line

tag: treatment

value: STL427944 and DOX


title: F_5_p


title: FigS3DE_22005_75IP

description: Arrested in G2 (Nocodazole) at 37˚C


title: Fig3C_24574WCE

description: Arrested in G2 (Nocodazole) at 35.5˚C

value: sac_cer strain:K24574


title: AIDcre Mettl3flox 1w Ctrl DZ rep2 MARS-seq

value: Germinal center dark zone B cells


title: F_5_q

value: Peripheral Blood


title: KHA082120_014

description: U2OS human osteosarcoma cells with doxycycline-inducible expression of EGFP-FOXM1 fusion protein, adherent epithelial cells, treated with 0.1% DMSO (vehicle) for 24 hours, RNA purified immediately after treatment

source_name: C3Luc DMSO

value: DMSO


title: FigS3F_22005_75WCE

description: Arrested in G2 (Nocodazole) at 37˚C

value: sac_cer strain:K22005


title: KHA082120_013

description: HCT116 human colorectal cancer cell line, adherent epithelial cells, stable shRNA-mediated FOXM1 expression knockdown with lentiviral particles from Sigma (TRCN0000015546) and subsequent selection with 1.5 ug/mL puromycin,  treated with 0.2% DMSO (vehicle) for 24 hours, RNA purified immediately after treatment

source_name: HCT116 FOXM1KD


title: AIDcre Mettl3flox 1w cKO LZ rep3 MARS-seq

value: AIDcre Mettl3-flox/flox


title: AIDcre Mettl3flox 1w Ctrl DZ rep1 MARS-seq


title: Fig3C_24574IP

description: Arrested in G2 (Nocodazole) at 35.5˚C

value: anti-PK antibody (Bio-Rad)


title: KHA082120_012

description: HCT116 human colorectal cancer cell line, adherent epithelial cells, treated with 50 uM of STL427944 and 50 uM of 5-fluorouracil for 24 hours, RNA purified immediately after treatment

source_name: HCT116 STL+5FU

value: STL427944 and 5-fluorouracil


title: F_4_r

value: Bulk CD4 T cells


title: Fig3C_24568WCE

description: Arrested in G2 (Nocodazole) at 35.5˚C

value: sac_cer strain:K24568

value: can_gla strain:K23308


title: HP1c^f04929, replicate two

city: Birmingham

first: Nicole

last: Riddle

state: AL

address: 506 10th St S

department: Biology

institute: University of Alabama at Birmingham

data_processing:
Basecall performed using bcl2fastq version 2.18.0.12
Fastq quality was assessed using fastqc
fastq files were aligned to reference genome dmel r6.25 using STAR (version 2.5.2) with default parameters
Aligned bam files were indexed using Picard BuildBamIndex, with default parameters
Transcript counts were calculated from indexed bam files using HTSeq-count (version 0.6.1)
Genome_build: dmel r6.25
Supplementary_files_format_and_content: transcript counts in tab delimited text format

organism: Drosophila melanogaster

source_name: third instar larvae

growth_protocol: Drosophila were grown at 25C in an incubator with ~70% humidity on Jazzmix food (Fisher Scientific)

extract_protocol:
Total RNA was isolated using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Third instar larvae

tag: strain/genotype


title: Fig3C_24568IP

description: Arrested in G2 (Nocodazole) at 35.5˚C


title: HP1c^f04929, replicate one


title: KHA082120_011

description: HCT116 human colorectal cancer cell line, adherent epithelial cells, treated with 50 uM of STL427944 for 24 hours, RNA purified immediately after treatment

source_name: HCT116 STL


title: Fig3C_22005WCE

description: Arrested in G2 (Nocodazole) at 35.5˚C

value: none (input)


title: BS-seq_osrdr2-6_se

description: fem1-6_se Bs-seq

data_processing:
Low-quality sequences(q<20) and adapters were trimmed using trimmomatic.
Reads were mapped to MSU7.0 using bismark with default parameters
Genome_build: MSU 7.0
Supplementary_files_format_and_content: tdf

organism: Oryza sativa

source_name: seedling

growth_protocol: RIce plants grown in soil in Hainan province

extract_protocol:
genomic DNA was extrated using CTAB method.
Genomic DNA was sonicated and then end-repaired with End repair Enzyme Mix. The blunt-ended DNA were treated with Klenow fragment and dATP to yield a proruding3-"A" and cytosine-methylated adaptors from Illumina were ligated according to manufacture's instructions.

tag: cultivar

value: Japponica

value: seedling


title: Fig3C_22005IP

description: Arrested in G2 (Nocodazole) at 35.5˚C


title: KHA082120_010

description: HCT116 human colorectal cancer cell line, adherent epithelial cells, treated with 50 uM of 5-fluorouracil for 24 hours, RNA purified immediately after treatment

source_name: HCT116 5FU


title: BS-seq_Nip_se_rep2

description: Nip_se_rep2 Bs-seq

value: wildtype


title: AIDcre Mettl3flox 1w cKO DZ rep3 MARS-seq


title: KHA082120_015

description: U2OS human osteosarcoma cells with doxycycline-inducible expression of EGFP-FOXM1 fusion protein, adherent epithelial cells, pre-treated with 1 ug/mL doxycycline for 16 hours, treated with 1 ug/mL doxycycline and 0.1% DMSO (vehicle) for 24 hours, RNA purified immediately after treatment

source_name: C3Luc Doxy

value: DMSO and DOX


title: AIDcre Mettl3flox 1w cKO LZ rep2 MARS-seq

value: Germinal center light zone B cells


title: KHA082120_009

description: HCT116 human colorectal cancer cell line, adherent epithelial cells, treated with 0.2% DMSO (vehicle) for 24 hours, RNA purified immediately after treatment

source_name: HCT116 DMSO


title: AIDcre Mettl3flox 1w cKO DZ rep2 MARS-seq

value: Germinal center dark zone B cells


title: Fig3C_22001WCE

description: Arrested in G2 (Nocodazole) at 35.5˚C

value: sac_cer strain:K22001


title: BS-seq_Nip_se_rep1

description: Nip_se_rep1 Bs-seq


title: KHA082120_008

value: STL427944 and DOX


title: BS-seq_osrdr2-6_pa

description: fem1-6_pa Bs-seq

source_name: young panicle

value: panicle


title: AIDcre Mettl3flox 1w cKO LZ rep1 MARS-seq

value: AIDcre Mettl3-flox/flox


title: AIDcre Mettl3flox 1w cKO DZ rep4 MARS-seq


title: Fig3C_22001IP

description: Arrested in G2 (Nocodazole) at 35.5˚C

value: anti-PK antibody (Bio-Rad)


title: KHA082120_007


title: AIDcre Mettl3flox 1w cKO DZ rep1 MARS-seq


title: smallRNA_osrdr2-6_se

description: fem1-6_se sRNA-seq

data_processing:
Adapter sequences were trimed and clean reads with sizes ranging from 18 to 35 were mapped to MSU7.0 using Bowtie with parameter -v 0.
Annotated structure RNAs were excluded.
Read counts were normalized to RPTM.
Genome_build: MSU7.0
Supplementary_files_format_and_content: RPTM

extract_protocol:
RNA was extrated using TRIzol method.
18-35nt small RNA was cut from PAGE gel.


title: KHA082120_006

value: DMSO


title: BS-seq_Nip_pa_rep2

description: Nip_pa_rep2 Bs-seq


title: Fig2D_24564WCE

description: Cycling cells

value: sac_cer strain:K24564


title: Fig2D_24564IP

description: Cycling cells


title: KO LPS 24hr 6

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Lung tissue from an animal with liver-specific knockout of Stat3, challenged with LPS, and exposed to intracheal E. coli for 24h.

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (version 2.5.3a).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 92 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.3), and alignment quality was assessed using RSeQC (version 2.6.4).
Regularized logarithm (rlog) transformation was accomplished using the DESeq2 R package (version 1.19.49) and R version 3.5.0.
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: lung tissue

growth_protocol: Mice with homozygous floxed alleles for STAT3 were crossed with mice expressing albumin-driven Cre-recombinase. Results from hepSTAT3-/- mice were compared to those from littermate controls lacking Cre-recombinase. Both male and female mice were used, all between 6 and 15 weeks of age, and results were collected over a minimum of two independent experiments. All animal protocols were approved by the Boston University Institutional Animal Care and Use Committee.

extract_protocol:
Lungs were homogenized in RLT buffer in bullet blender tubes, then instructions and items from Rneasy Mini Kit (Qiagen #74104) and Rnase-free Dnase set (Qiagen #74124) were followed to isolate whole lung RNA.
The libraries were prepared from 200 ng total RNA enriched for mRNA using Illumina’s TruSeq Stranded mRNA Library Preparation kit (Illumina, USA).

treatment_protocol: Mice were given an intraperitoneal (i.p.) injection of 1 mg/kg of body weight of ultrapure lipopolysaccharide (LPS-EB from E. coli O111:B4; catalog code tlrl-eblps; InvivoGen) or saline.  After 18h, intratracheal (i.t.) instillations were performed. Briefly, mice were anesthetized with ketamine (50 mg/kg of body weight) and xylazine (5 mg/kg), administered by i.p. injection. A 24-gauge catheter was inserted into the exposed trachea, and a 50 ul bolus of saline containing 10^6 CFU of Escherichia coli (serotype O6:K2:H1, ATCC 19138) was instilled into the left bronchus. Mice were euthanized using an isoflurane overdose at the time of tissue collection.

value: lung

value: liver-specific Stat3 knockout

tag: challenge

value: LPS

tag: exposure

value: 24hr intratracheal E. coli


title: KHA082120_005


title: Fig2D_24689WCE

description: Cycling cells

value: sac_cer strain:K24689

value: can_gla strain:K23308

value: none (input)


title: KO LPS 24hr 4


title: smallRNA_Nip_se_rep1

description: Nip_se_rep1 sRNA-seq

value: Japponica

value: seedling

value: wildtype


title: KHA082120_004

value: STL427944 and 5-fluorouracil


title: smallRNA_Nip_se_rep2

description: Nip_se_rep2 sRNA-seq


title: KHA082120_003


title: smallRNA_osrdr2-6_pa

description: fem1-6_pa sRNA-seq


title: KO LPS 24hr 11


title: KO LPS 24hr 7


title: FigD_24562WCE

description: Cycling cells

value: sac_cer strain:K24562


title: Fig2D_24689IP

description: Cycling cells


title: KHA082120_002


title: smallRNA_Nip_pa_rep2

description: Nip_pa_rep2 sRNA-seq

value: panicle


title: WT LPS 24hr 5

description: Lung tissue from an animal with wild-type Stat3, challenged with LPS, and exposed to intratracheal E. coli for 24h.

value: wild-type


title: KHA082120_001


title: WT LPS 24hr 6


title: Fig2C_24680IP

description: Cycling cells

value: sac_cer strain:K24680

value: anti-PK antibody (Bio-Rad)


title: iPSCE20-2

data_processing:
Fastq reads were trimmed for adaptor sequence  and aligned to human reference genome (hg19) using TopHat with default parameters
Counting and FPKM values were calculated with cuffquant and cuffnorm respectively with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: xlsx files include FPKM values for each Sample

source_name: eosinophil cells

growth_protocol: Human embryonic stem cells (H1) were obtained from Wicell (NIH: hESC-10-0043), and their usage was annually approved. H1 cells were cultured in Matrigel (BD Biosciences, Cat: 354230)-coated plates with pluripotent stem cell culture medium (PSCM, PSCeasy, Beijing CELLAPY Biotechnology) under 20% O2 and 5% CO2 at 37 °C. H1 cells were passaged by treatment with 0.5 μM EDTA (Gibco, Cat: 25300-062) for 5-6 min at 37 °C, and cells were collected and split at 1 to 6 - 1 to 10 ratios with pluripotent stem cell culture medium containing 5 μM Y-27632 (Selleck, Cat# S1049). iPS cells (iPS-#7) were purchased from Cauliscell Biotechnology (Cat: 200101) and were cultured in Matrigel-coated plates with pluripotent stem cell culture medium (PSCeasy, Beijing CELLAPY Biotechnology). iPS cells were passaged by splitting at ratios of nearly 1 to 6 following treatment with 0.5 μM EDTA for 5-6 min at 37 °C, and then the cells were collected and plated with pluripotent stem cell culture medium containing 5 μM Y-27632.   Mesoderm and hematopoietic endothelial (HE) cell differentiation were induced as previously described with optimizing conditions (Wang et al., 2012). Briefly, 6x105 H1 cells were seeded in a 6-well ultralow attachment plate (Corning, Cat: 3471) to form embryonic bodies (EBs); they were grown in pluripotent stem cell culture medium (PSCM, PSCeasy, Beijing CELLAPY Biotechnology) containing 5 μM Y276532. The next day, the medium was changed to RPMI 1640 (Thermo Fisher Scientific) that was supplemented with B27 without vitamin A (Thermo Fisher Scientific, Cat: 12587010), 50 μg/ml ascorbic acid (Sigma, Cat: A8960-5G), 20 ng/ml recombinant human bone morphogen protein-4 (BMP4, StemImmune LLC, Cat: HST-B4-0100), 1% GlutaMAX, 1% PS, 1% NEAA and 0.1 mM 1-thioglycerol (Sigma, Cat: M6145-25 ml). After 2 days of mesodermal induction, the differentiated EBs were cultured with RPMI 1640 supplemented with B27 without vitamin A, 50 μg/ml ascorbic acid, 5 ng/ml BMP4, 50 ng/ml human vascular endothelial growth factor (VEGF, StemImmune LLC, Cat: HVG-VF5-1000), 50 ng/ml human basic fibroblast growth factor (bFGF, Origene, Cat: TP750002), 1% GlutaMAX, 1% PS, 1% NEAA and 10 μM SB-431542 (Selleck, Cat: S1067). Next, for hematopoietic induction, the culture medium was changed on day 6 to IMDM (Thermo Fisher Scientific) supplemented with B27 without vitamin A, 50 μg/ml ascorbic acid, 5 ng/ml BMP4, 10 ng/ml VEGF, 20 ng/ml recombinant human stem cell factor (SCF, StemImmune LLC, Cat: HHM-SF-1000), 30 μM NAC (Sigma, Cat: A7250-5G), 2 μM minocycline hydrochloride (Selleck, Cat: 3268), 1% GlutaMAX, 1% PS and 1% NEAA. On day 12, eosinophil induction medium was used, which consisted of IMDM supplemented with B27 without vitamin A, 30 μM NAC, 2 μM minocycline hydrochloride, 10 ng/ml human recombinant interleukin-3 (IL3, StemImmune LLC, Cat: HCT-I3-1000), 10 ng/ml human recombinant interleukin-5 (IL5, Novoprotein, Cat: CI59), 1% GlutaMAX, 1% PS and 1% NEAA. The culture medium was changed every 2 days.During H1 differentiation, total RNA was isolated from cultured cells on day 0 (H1), day 12 (E0), day 16 (E4), day 20 (E8), day 24 (E12), day 28 (E16), and day 32 (E20) using RNeasy Plus Micro kit (Qiagen, 74034).For iPSC differentiation, total RNA from day 0 and day 28 (E20) cultured cells was isolated and sequenced via the same method used for H1 cells.   Human primary naïve eosinophils were isolated based on anti-CD16-negative selection protocol (Wacht et al., 2018) via certain modifications. Briefly, cord blood unit was diluted by sterile PBS, aliquoted gently to human lymphocyte separation medium (DRKEWE, Cat: DKW-KLSH-0100), and centrifuged at 1500 rpm for 20 min according to the manufacturer’ s protocol to get blood cells separated in different layers. Cell pellets in the bottom layer, which contained mainly granulocytes and red blood cells, were collected and suspended in 1×RBC lysis buffer (Biolegend, Cat: 420301) to lyse the red blood cells according to the product manual. After lysis of red blood cells, the remaining cells were mainly granulocytes. They were washed twice with PBS, centrifuged at 1500 rpm for 5 min. Cell pellets were then collected and stained with BV421 anti-human CD45 (Biolegend, Cat: 304032) and PE-Cy7 anti-human CD16 (Biolegend, Cat: 302016) according to the product manual. Then the CD45+CD16- cell population were isolated by the flow cytometer (MoFlo XDP) and collected in sterile PBS. These CD45+CD16- cells were regarded as primary naïve eosinophils.

treatment_protocol: During H1 differentiation, total RNA was isolated from cultured cells on day 0 (H1), day 12 (E0), day 16 (E4), day 20 (E8), day 24 (E12), day 28 (E16), and day 32 (E20) using RNeasy Plus Micro kit (Qiagen, 74034).For iPSC differentiation, total RNA from day 0 and day 28 (E20) cultured cells was isolated and sequenced via the same method used for H1 cells.Human primary naïve eosinophils were isolated based on anti-CD16-negative selection protocol (Wacht et al., 2018) via certain modifications.

value: pluripotent stem cell derived eosinophil cells

tag: differention time(days)


title: FigD_24562IP

description: Cycling cells


title: Fig2C_24680WCE

description: Cycling cells


title: iPSCE20-1


title: Fig2C_24678WCE

description: Cycling cells

value: sac_cer strain:K24678


title: KO LPS 0hr 3

description: Lung tissue from an animal with liver-specific knockout of Stat3, challenged with LPS.

value: lung

value: liver-specific Stat3 knockout

value: no exposure


title: KO LPS 0hr 2

value: LPS


title: iPSC-2

source_name: induced pluripotent stem cell

value: induced pluripotent stem cell


title: RNA-seq_Nip_se_rep2

description:
Nip_se_rep2 mRNA-seq
mRNA sequencing

data_processing:
Low-quality reads had been eliminated.
All reads were mapped onto the O.sativa genome (MSU version 7.0) by Tophat.
Expression level were normalized through fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: O.sativa genome (MSU version 7.0)
Supplementary_files_format_and_content: FPKM in tdf formatted file

extract_protocol:
RNA was extrated using TRIzol method.
1.Total RNA used DNaseI to digest DNA, and enriched mRNA using magnetic beads with Oligo(dT).  2.Adding reagent in Thermomixer to interrupt mRNA into short fragments.  3.The fragmented mRNA was used as template to synthesize the first strand of cDNA, and then synthesized the second strand.  4.Purified by using the kit, and repaired the adhesive termination, added the base "A" and adapter in the CDNA 3'end, then selected 200-300bp fragments and performed PCR amplification.   5.The libraries were checked with Agilent 2100 Bioanalyzer and ABI Real-Time PCR System, the qualified libraries were sequenced using sequencing platform.


title: Fig2C_24678IP

description: Cycling cells

source_name: Saccharomyces cerevisiae cells

value: can_gla strain:K23308


title: RNA-seq_Nip_se_rep1

description:
Nip_se_rep1 mRNA-seq
mRNA sequencing

value: Japponica


title: KO LPS 0hr 14


title: iPSC-1


title: WT DSB t2 - replicate 1

city: PARIS

first: Helene

last: Bordelet

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

description: Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format

data_processing:
Reads were aligned and the contact data processed using Hicstuff 9. Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 in its most sensitive mode against the S. cerevisiae W303 reference genome (GCA_002163515.1). The reference was deleted for the URA3 and LYS2 genes, which are either absent or partially duplicated in our strains, respectively. Each uniquely mapped read was assigned to a restriction fragment. Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in ref. 10. PCR duplicates (defined as paired reads mapping at exactly the same position) were discarded. Contact maps were generated with the “view” function of Hicstuff and normalized using the iterative correction and eigenvector decomposition (ICE) procedure11. Bins were set at either 1 or 2 kb for single chromosomes, or 5 kb for multiple chromosomes, log10 transformed, and rendered.
Supplementary_files_format_and_content: cool

organism: Saccharomyces cerevisiae W303

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. 2020. Quenching of formaldehyde with 300 mM glycine was performed at room temperature for 20 min. Most Hi-C experiments were performed with the Arima Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions, except those presented in Supplementary Fig. 3, performed as in Dauban et al. 2020 with a single DpnII restriction digestion.
TruSeq Nano DNA Library Prep (Illumina, cat. FC-121-9010DOC) or Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems (A38606024).

tag: strain

value: DSB 2 hr


title: CBE-2

value: cord blood-derived primary eosinophil


title: KO LPS 0hr 11


title: Fig2C_21388WCE

description: Cycling cells

tag: sac_cer strain

value: sac_cer strain:K21388

value: none (input)


title: Fig2C_21388IP

description: Cycling cells

tag: can_gla strain


title: RNA-seq_osrdr2-6_se_rep2

last: Wang

address: Weigang No.1

institute: Nanjing Agricultural University

description:
fem1-6_se_rep2 mRNA-seq
mRNA sequencing

value: seedling


title: rad17 DSB  t4 nocodazole block replicate 1 [NovaSeq 6000]

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB27_1_2_merged_1kb.cool

value: DSB 4 hr + Nocodazole


title: WT LPS 0hr 5

description: Lung tissue from an animal with wild-type Stat3, challenged with LPS.

value: wild-type


title: mre11 DSB  t4 nocodazole block [NovaSeq 6000]

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB26_1_2_merged_1kb.cool


title: RNA-seq_osrdr2-6_se_rep3

description:
fem1-6_se_rep3 mRNA-seq
mRNA sequencing


title: WT LPS 24hr 9

value: 24hr intratracheal E. coli


title: RNA-seq_osrdr2-6_se_rep1

description:
fem1-6_se_rep1 mRNA-seq
mRNA sequencing


title: Fig2BS2B_19624WCE

description: Arrested in G2 (Nocodazole) at 25˚C

value: sac_cer strain:K19624

tag: antibody


title: Fig2BS2B_19624IP

description: Arrested in G2 (Nocodazole) at 25˚C

value: anti-PK antibody (Bio-Rad)


title: WT LPS 0hr 4

value: lung


title: WT DSB  t4 nocodazole block replicate 1 [NovaSeq 6000]

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB25_1_2_merged_1kb.cool


title: CBE-1

tag: cell type


title: WT LPS 0hr 16


title: E20-2

value: pluripotent stem cell derived eosinophil cells


title: Fig2BS2B_22009WCE

description: Arrested in G2 (Nocodazole) at 25˚C

value: sac_cer strain:K22009


title: E20-1


title: sml1 DSB t4 + nocodazole - replicate 2


title: mec1 sml1 DSB t4 + nocodazole - replicate 2


title: WT saline 0hr 17

description: Lung tissue from an animal with wild-type Stat3, challenged with saline.

value: saline

value: no exposure


title: E16-2


title: Fig2BS2B_22009IP

description: Arrested in G2 (Nocodazole) at 25˚C

value: can_gla strain:K23308


title: Fig2BS2B_22005WCE

description: Arrested in G2 (Nocodazole) at 25˚C

value: sac_cer strain:K22005


title: E16-1


title: pds5-AID DSB t4 on chrIV + nocodazole - replicate 1


title: WT saline 0hr 12


title: pds5-AID rad17 DSB t4 on chrIV + nocodazole - replicate 1


title: Fig2BS2B_22005IP

description: Arrested in G2 (Nocodazole) at 25˚C


title: WT saline 0hr 5


title: WT saline 0hr 2


title: E12-1


title: Fig2AS2A_22009IP

description: Arrested in G2 (Nocodazole) at 37˚C


title: E8-2

source_name: hematopoietic progenitor cells

value: pluripotent stem cell derived hematopoietic progenitor cells


title: Fig2AS2A_22005WCE

description: Arrested in G2 (Nocodazole) at 37˚C


title: WT DSB t4 (induced while releasing from G1 block) - replicate 2

value: DSB 4 hr (after G1 release)


title: WT DSB t4 +IAA (induced while releasing from G1 block)

value: DSB 4 hr + IAA (after G1 release)


title: WT LPS 0hr 3

value: LPS


title: E4-2


title: Fig2AS2A_22005IP

description: Arrested in G2 (Nocodazole) at 37˚C


title: pds5-AID DSB t4 on chrIV + nocodazole - replicate 2


title: E0-2


title: Fig2AS2A_22001WCE

description: Arrested in G2 (Nocodazole) at 37˚C

value: sac_cer strain:K22001

value: none (input)


title: rad17 DSB t4 on chrIV + nocodazole - replicate 2

value: DSB 4 hr + Nocodazole


title: pds5-AID rad17 DSB t4 on chrIV + nocodazole - replicate 2


title: E12-2


title: WT DSB t4 on chrIV + nocodazole


title: Fig2AS2A_21999WCE

description: Arrested in G2 (Nocodazole) at 37˚C

value: sac_cer strain:K21999


title: E0-1


title: pds5-AID DSB t4 on chrIV

value: DSB 4 hr


title: Fig2AS2A_22009WCE

description: Arrested in G2 (Nocodazole) at 37˚C


title: Fig2AS2A_21999IP

description: Arrested in G2 (Nocodazole) at 37˚C

value: anti-PK antibody (Bio-Rad)


title: rad17 DSB t4 on chrIV + nocodazole - replicate 1


title: H1-1

source_name: pluripotent stem cell

value: pluripotent stem cell


title: E8-1


title: E4-1


title: Fig2AS2A_22001IP

description: Arrested in G2 (Nocodazole) at 37˚C


title: H1-2


title: Blastula_Input_rep2

status: Public on Jul 20 2021

city: Caen

first: Lorane

last: Le Franc

address: Université de Caen Normandie Esplanade de la Paix

institute: UMR BOREA

data_processing:
Read quality was evaluated using FastQC (v.0.11.7) and MultiQC (v.1.7) and adaptor sequences and low-quality reads were removed using Trimmommatic (v.0.38) in Input and IP sequencing data
The remaining reads were aligned to oyster genome v.9 (GCF_000297895.1) and uniquely mapped reads per gene were counted using STAR (v.2.7.3a; -quantMode GeneCounts)
The expression level in all Input samples was expressed in TPM (Transcripts per Million) (Li et al. 2010)
The identification of m6A-enriched peaks were performed on uniquely mapped reads of mRNA using Samtools (v.1.9) and MeTPeak R package (Cui et al. 2016a) (FDR < 5%) on all developmental stages of IP and Input samples serving as control.
The methylation levels of these m6A-enriched methylated RNAs correspond to the fold-change of IP/Input provide by MeTPeak
Genome_build: GCF_000297895.1
Supplementary_files_format_and_content: tab delimited text files include TPM values for each developmental stages for the two distinct development
Supplementary_files_format_and_content: tab delimited xls files are peak text files

organism: Magallana gigas

source_name: developmental stage

growth_protocol: Mature gametes are collected and incubated in sterile sea water at 21°C and embryonic stages were collected after determination by light microcopy observation. Oocytes (immediately before sperm addition), fertilized oocytes (after expulsion of the secondary polar body), two to eight cell embryos (ca. 1.5 hours post fertilization (hpf)), morula (ca. 4 hpf), blastula (ca. 6 hpf), gastrula (ca. 10 hpf), trochophore (ca 16 hpf) and D larvae (ca. 24 hpf) were collected. For pediveliger and spat stages, the non-sampled D-larvae were collected and reared in flow-through rearing system at 25 °C in sterile sea water and collected at 20 days post fertilization (Pediveliger) and 25 days post fertilization (Spat).

extract_protocol:
For each stage, 3 million embryos and 100 mg of pediveliger and spat were collected. Total RNA was extracted using Trizol reagent. m6A-RNAs were isolated with an antibody anti-m6A (ABE572, Millipore) followed by low/high salt buffer washing.
The amount of 3.5 µl of IP and the equivalent amount of 50 ng of Input RNAs were used for the library construction according to the manufacturer’s protocol without fragmentation option of the SMARTer Stranded Total RNA-Seq Kit v.2  (634418, Pico Input Mammalian). Paired-end 150-bp sequencing of Input and IP cDNAs of each sample were conducted on Illumina HiSeq 4000 platform at the Genome Quebec innovation Center (McGill University, Montréal, Canada).

tag: developmental stage

value: embryo

tag: merip antibody


title: Pediveliger_Input_rep2

value: larva


title: Trochophore_Input_rep2


title: Morula_Input_rep2


title: Pool_Input_rep2

value: Pool of developmental stages


title: Pool_IP_rep2

value: m6A (Millipore, ABE572)


title: Spat_Input_rep2

value: Juvenile


title: Pool_Input_rep1


title: D-larva_Input_rep2


title: Pool_IP_rep1


title: Gastrula_Input_rep2


title: D-larva_IP_rep2


title: Oocyte_Input_rep2

value: Oocyte


title: Pediveliger_IP_rep2


title: Fertilized_oocyte_Input_rep2


title: Spat_IP_rep2


title: maoSMC AdN5_3

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: gene expression of murine aortic smooth muscle cells in which overexpression of Nfat5 was achieved

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Mouse MoGene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: murine aortic smooth muscle cells overexpressing NFAT5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: murine aortic VSMCs were cultured in DMEM +15% FCS and propagated 1:3

extract_protocol: RNA was extracted from VSMCs by utilizing the Qiagen mini RNA extraction kit  following man. instr.

treatment_protocol: VSMCs were exposed to adenovirus for 24 hours and treated with cholesterol (10µg/ml) for further 72 hours before RNA extraction

value: murine aortic Vascular Smooth Muscle Cells (VSCMs)

tag: genotype/variation

value: NFAT5 overexpression

value: cholesterol (10µg/ml) for 72hrs


title: Trochophore_IP_rep2


title: maoSMC AdN5_2


title: maoSMC AdN5_4


title: maoSMC AdN5_1


title: maoSMC AdPl_2

description: gene expression of murine aortic smooth muscle cells

source_name: murine aortic smooth muscle cells

value: Control


title: maoSMC AdPl_4


title: Gastrula_IP_rep2


title: maoSMC AdPl_1


title: Blastula_IP_rep2


title: Morula_IP_rep2


title: 2/8cells_Input_rep2


title: 2/8cells_IP_rep2


title: maoSMC AdPl_3


title: Pediveliger_Input_rep1


title: D-larva_Input_rep1


title: Blastula_Input_rep1


title: Morula_Input_rep1


title: Trochophore_Input_rep1


title: Fertilized_oocyte_IP_rep2


title: Gastrula_Input_rep1


title: Fertilized_oocyte_Input_rep1


title: 2/8cells_Input_rep1


title: Oocyte_Input_rep1


title: D-larva_IP_rep1


title: Spat_IP_rep1


title: Oocyte_IP_rep2


title: Trochophore_IP_rep1


title: Gastrula_IP_rep1


title: Blastula_IP_rep1


title: Pediveliger_IP_rep1


title: 2/8cells_IP_rep1


title: Oocyte_IP_rep1


title: Spat_Input_rep1


title: HKMT-3

city: Lyon

first: Pauline

last: Bade

address: 40 avenue Tony Garnier

institute: Evotec LYON ID SAS

description: test

data_processing:
The normalization was performed according to the manufacturers instructions and their web-hosted software https://apps.thermofisher.com/apps/spa/#/dashboard
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: Taqman probes

source_name: PMA-differentiated THP-1 cell infected with HKMT

label_protocol: Reverse transcription was performed from 500 ng total RNA using SuperScript VILO cDNA Synthesis Kit (Invitrogen). PCR were performed using TaqMan Fast Universal PCR Master Mix (2X), no AmpErase UNG (Applied Biosystem) following the Manufacturer’s instructions. Quantitative real-time PCR  were performed with the QuantStudio 12K Flex (Applied Biosystems) with a 2 min hold at 50°C, a 10 min hold at 92°C, then 40 cycles of 3s 95°C denaturation followed by 30s of 60°C extention.

extract_protocol: Total RNA was extracted with Maxwell® RSC miRNA Tissue Kit  (Promega)

value: PMA-differentiated THP-1 cell

tag: activation agent

value: HKMT

tag: time

value: 2 days


title: HKMT-4

description: test


title: HKMT-2

description: test


title: HKMT-1

description: test


title: M.marinum-4

description: test

source_name: PMA-differentiated THP-1 cell infected with M. marinum

value: M. marinum


title: M.marinum-2

description: test


title: M.marinum-1

description: test


title: Morula_IP_rep1


title: Fertilized_oocyte_IP_rep1


title: Mtb-4

description: test

source_name: PMA-differentiated THP-1 cell infected with H37Rv


title: Mtb-2

description: test


title: Mtb-3

description: test


title: Ctrl-12-HKMT

description: Control

source_name: PMA-differentiated THP-1 cell uninfected


title: Ctrl-11-HKMT

description: Control


title: MLLAF9-shATF3-Rep2

city: St Louis

first: Stephen

last: Sykes

address: 660 South Euclid Avenue

department: McDonnell Pediatric Research Building, Room 5102

institute: Washington University in St Louis

data_processing:
fastq files was generated at the basespace cloud
fastq files was aligned to mm10 using HISAT2 to generate bam files
Counts aligns reads per gene with HTSeq
Differentially expressed gene list was obtained by using DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq-normalized read counts
Supplementary_files_format_and_content: DEseq2-differentially expressed genes

source_name: Fox Chase Cancer Center

growth_protocol: Cultured murine MLL-AF9 cells

extract_protocol:
RNA was extracted with Trizol, and purified via Qiagen RNeasy column
NEB stranded mRNA-seq kit was used
mRNA was enriched by using oligoT beads and heat fragmentated, then reverse transcribled to cDNA.  Illumina adapters were ligated to the cDNA and PCR was performed to get the final library.

treatment_protocol: cells were infected with a shNT or shAtf3 lentivirus; and harvested for RNA-Seq

tag: cell line

value: shAtf3 lentivirus


title: MLLAF9-shATF3-Rep3


title: MLLAF9-shATF3-Rep1


title: Ctrl-9-HKMT

description: Control


title: Ctrl-6-M.marinum

description: Control


title: Ctrl-5-M.marinum

description: Control


title: Ctrl-8-M.marinum

description: Control


title: MLLAF9-shNT-Rep3

value: shNT lentivirus


title: Ctrl-4-Mtb

description: Control


title: Ctrl-3-Mtb

description: Control


title: Ctrl-2-Mtb

description: Control


title: Ctrl-1-Mtb

description: Control


title: MLLAF9-shNT-Rep2


title: MLLAF9-shNT-Rep1


title: E12.5 inv2 posterior proximal forelimb, replicate 1 CR_HOXD13

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

description: CUT&RUN

data_processing:
Library strategy: CUT&RUN
CUT and RUN reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). Adapters and bad-quality bases were removed with Cutadapt version 1.16 (Martin, 2011). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), (-I 0 -X 1000 –fr –dovetail –very-sensitive).
Reads with mapping quality below 30 or not properly paired were removed from the analysis. PCR duplicates were removed.
The output BAM file was converted to BED using bamtobed bedtools v2.18.2 (Quinlan, 2014).
The coverage was obtained as the output of MACS2 (v2.1.1.20160309) (Zhang et al., 2008) (--format BED --keep-dup all --bdg --nomodel --extsize 200 --shift 100).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig: coverage from macs2
narrowPeak: narrowPeak from macs2

source_name: posterior proximal forelimb

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

extract_protocol:
The forelimbs of embryos were dissected and placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min.
DNA isolated from the CUT&RUN protocol were prepared with KAPA HyperPrep reagents (07962347001) with 2.5ul of adaptors at 0.3uM and ligated for 1 hour at 20ºC. The DNA was amplified for fourteen cycles. Post-amplified DNA was cleaned and size selected using 1:1 ration of DNA:Ampure SPRI beads (A63881) followed by an additional 1:1 wash and size selection with HXB. HXB is equal parts 40% PEG8000 (Fisher FIBBP233) and 5M NaCl. The anti-CTCF  antibody is Active Motif 61311, and the anti-HOXD13 antibody is Abcam Ab19866.

treatment_protocol: No treatment

tag: age

tag: genotype

value: anti-HOXD13 (Abcam Ab19866)

tag: tissue

value: posterior proximal forelimb


title: Mtb-1

description: test


title: Ctrl-10-HKMT

description: Control


title: E12.5 wild type distal forelimb CR_CTCF

description: CUT&RUN

source_name: distal forelimb

value: wild-type

value: anti-CTCF (Active Motif 61311)

value: distal forelimb


title: E12.5 inv2 distal forelimb CR_CTCF

description: CUT&RUN


title: E12.5 inv2 posterior proximal forelimb, replicate 2 CR_HOXD13

description: CUT&RUN


title: E12.5 inv2 proximal forelimb CR_CTCF

description: CUT&RUN

source_name: proximal forelimb

value: proximal forelimb


title: E12.5 wild type proximal forelimb CR_CTCF

description: CUT&RUN


title: E12.5 inv2 distal forelimb capture Hi-C

data_processing:
CUT and RUN reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). First, adapters were removed using cutadapt version 1.6 (Martin, 2011) with the following parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC for R1 and -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT for R2.
They were then processed by using hicup version 6.1.0 with the bowtie2 version 2.2.6 (Langmead and Salzberg, 2012) and SAMtools version 1.2, with mm10 as reference genome and GATC as restriction enzyme recognition sequence.
The pairs were next converted from bam to tabulated files, with the position of the middle of the fragment to which hicup assigned the read, by using an ad hoc python script (script available at https://github.com/lldelisle/scriptsForBoltEtAl2021).
Only valid pairs with both MAPQ above 30 were kept.
Then, pairs with both mates in the capture region (mm10, chr2:72402000-77000000) were extracted and processed with cooler to obtain a balance matrix of the capture region with 5-kb bins.
Genome_build: mm10
Supplementary_files_format_and_content: pairs: contains every valid pair for each dataset in the juicebox format: Each line is a pair: <readname> <str1> <chr1> <pos1> <frag1>   <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse)
cool: contains the iced matrix in the capture region at 5kb resolution

extract_protocol:
The forelimbs of embryos were dissected and placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min. Collagenase treated samples were cross-linked with 1% formaldehyde (ThermoFisher 28908) for 10 minutes at room temperature and stored at -80º until further processing as previously described (Yakushiji-Kaminatsui et al., 2018)
Following the Hi-C protocol, ligated DNA fragments were processed throught the Agilent SureSelectXT protocol to enrich for fragments coming from the probe region chr2:72240000-76840000 (mm9).
SureSelectXT


title: E12.5 inv2 forebrain capture Hi-C

source_name: forebrain

value: forebrain


title: AIDcre Mettl3flox 2w Ctrl LZ rep2 MARS-seq

data_processing:
Mars-seq: Reads were trimmed using Cutadapt
Mars-seq and m6A-IP: Reads were aligned to the genome using STAR
Mars-seq: Quantification was done using htseq-count as previously described in R. Kohen, BMC Bioinformatics, 2019.
m6A-IP: Normalization of paired libraries insert size was performed using in-house python scripts, between pairs of INPUT-IP samples. Alignment sorting and indexing were performed separately with samtools (V. 1.3.1) (Li et al. Bioinformatics, 2009).
m6A-IP: Identification of putative m6A sites was performed by assigning peak over input (POI) and peak over median (POM) scores to each site, as previously published (Schwartz et al, Cell 2014)
Genome_build: Mars-seq: mm10, m6A-IP: mm9
Supplementary_files_format_and_content: Excel file with Deseq2 output
Supplementary_files_format_and_content: Text file with filtered m6A-peaks 1
Supplementary_files_format_and_content: Text file with filtered m6A-peaks 2

source_name: B cells

value: Germinal center light zone B cells

tag: mouse strain

value: AIDcre Mettl3-flox/+


title: E12.5 inv2 proximal forelimb capture Hi-C


title: E12.5 wild type forebrain capture Hi-C

value: wild type


title: E12.5 inv2 proximal forelimb ATAC-seq

data_processing:
ATAC-seq reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), (-I 0 -X 2000 --fr --dovetail --very-sensitive-local).
Reads with mapping quality below 30, mapping to mitochondria, or not properly paired were removed from the analysis. PCR duplicates were filtered using Picard (v1.56.0).
BAM file was converted to BED with bedtools version 2.27. Peak calling was done using MACS2 (v2.1.0.20151222) callpeak (--nomodel --shift 100 --extsize 200 --call-summits --keep-dup all).
The coverage was done using the center of the Tn5 insertion and extended on both sides by 20 bp (script available at https://github.com/lldelisle/scriptsForBoltEtAl2021)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig: coverage centered on the Tn5 insertion (20bp extended both sides)
narrowPeak: narrowPeak from macs2

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


title: E12.5 wild-type proximal forelimb ATAC-seq


title: E12.5 inv2 distal forelimb ATAC-seq


title: Nat_ATAC_23

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

institute: SAHMRI

data_processing:
Reads were aligned to the mm10 mouse genome using Bowtie2.
Peaks were called using Genrich v0.6.
Counts per peak were generated using FeatureCounts v1.53p.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.featureCounts_mm10.txt: FeatureCounts output; Tab-delimited text files with raw peak counts for every peak for each sample.

source_name: Murine Dendritic Cells

extract_protocol:
50,000 cells per sample were lysed in 50µl ATAC-seq lysis buffer containing 0.1% NP-40, 0.1% Tween-20 and 0.001% digitonin (Promega) in 0.5mL tubes and nuclei pelleted via centrifugation. Nuclei were transposed using 2µl Tn5 transposase (Illumina) in 50µl 1x TD buffer for 30 minutes at 37°C.
Transposed DNA samples were purified using DNA Clean and Concentrator 5 columns (Zymo Research) prior to PCR amplification with adaptor-specific primers containing Illumina index sequences. Amplified libraries were cleaned up with DNA Clean and Concentrator 5 columns and libraries were quantified using a 4150 TapeStation system (Agilent) with High Sensitivity D1000 reagents. Following QC, libraries were sequenced on a NextSeq 500 Sequencer (Illumina) using a High-Output Flow Cell. 2x75bp.

value: Dendritic cells

tag: treatment

value: Mock/Not vaccinated


title: Nat_ATAC_24


title: Healthy sample 1

city: Houston

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

institute: UT Health Science Center at Houston

description: Healthy sample 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 with default parameters
Count values were calculated using htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

growth_protocol: Fibroblasts were cultured in DMEM containing 10% FBS (Sigma-Aldrich), penicillin/streptomycin (Sigma-Aldrich), plasmocin (Invivogen) and amphotericin B (Sigma-Aldrich). Passage 3 and 4 were used for all subsequent analysis.

extract_protocol: RNA was isolated using Trizol and the Qiagen RNeasy kit (Qiagen) according to the manufacturer’s instructions. RNA was stored at -80 °C.

treatment_protocol: Primary human lung fibroblasts were isolated directly from the upper half of the upper lobe close to apical regions from human lungs

tag: sample type

value: normal

value: lung

value: fibroblasts


title: IPF sample 4

description: IPF sample 4

source_name: ID no: 121

value: diseased


title: Healthy sample 2

description: Healthy sample 2


title: Healthy sample 3

description: Healthy sample 3


title: Healthy sample 4

description: Healthy sample 4


title: Nat_ATAC_20

value: BCG vaccinated


title: IPF sample 5

description: IPF sample 5

source_name: ID no. 127


title: Nat_ATAC_19


title: E12.5 wild type forebrain CR_CTCF

description: CUT&RUN

tag: strain


title: IPF sample 3

description: IPF sample 3

source_name: ID no: 120


title: IPF sample 2

description: IPF sample 2

source_name: ID no: 9


title: Nat_ATAC_17


title: IPF sample 1

description: IPF sample 1

source_name: ID no: 4


title: E13.5 wild-type forebrain ATAC-seq


title: Nat_ATAC_15

value: DTPw vaccinated


title: Nat_ATAC_18


title: Nat_ATAC_16


title: Nat_ATAC_14


title: Nat_ATAC_12


title: Nat_ATAC_11